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Hub contributors should use the Hub Track specific version of this document.
This document describes how to declare dataset display characteristics in the Genome Browser through trackDb settings. Introducing new datasets for display in the Browser requires declaring the location and format of the data and defining initial display characteristics. In many cases, you may need to choose how the displayed data (aka "track") may be selected and configured. These settings are declared in a simple text file format and stored in a database called the "track database", or trackDb for short.
The text file format for trackDb settings follow the simple "ra" rules which establish a "record" as a set of related settings in a "stanza" delimited by blank lines. The first line of each stanza typically establishes the "key". Each line in a stanza will contain a single word "setting" name and one or more words or numbers that follow are the setting's "value". All trackDb stanzas are keyed by "track" and most will have certain common settings followed by track specific settings. Here is an example:
track myFirstTrack type bed 6 shortLabel Example Data longLabel The data in this track is format "bed 6".
Every track should have
these four settings. The key of this track (myFirstTrack
)
is the name of the dataset. If the data is loaded into a MySQL
table then the track name is almost always the table name. If the
data is in one of the remote indexed file types (e.g. bigWig, bam,
etc.) then the name is typically the root file name. However, this
is a key to the track so it must be unique within the Genome Browser.
(Data hubs need only declare track names unique to their hub.)
After the "track" key, the most important setting for
defining a track is the "type". This tells the Browser
which format the data is in, defines how to display it, and determines
which options are available for fine control of that display.
The remainder of this document is divided into the following sections and should be used as a ready reference.
Many settings are valid only for certain types of tracks. These track types are described below along with the settings specific to their types.
bed/bigBed: Item or region tracksSome of the most common track types are those that highlight regions or items of varying size in a genome assembly. There are many variations to the "items" track, most of which are specified with a bed or bigBed format. These two formats are really a cluster of many formats all starting with three common fields (chromosome start end) and having optionally many more fields. For complete bed or bigBed format definitions please see the FAQ. |
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![]() type bed <3-12> [+/.] type bigBed <3-12> [+/.] |
![]() type bed5FloatScore type bedRnaElements type broadPeak type coloredExon type gvf type ld2 type narrowPeak type peptideMapping |
![]() bigDataUrl <url/relativePath> |
![]() colorByStrand <red,green,blue>
<red,green,blue> |
![]() compareGenomeLinks <db[.table[.column]]=label>
[db[.table[.column] =label …] |
![]() denseCoverage <maxVal> |
![]() labelOnFeature <on/off> |
![]() exonArrows <on/off> |
![]() exonNumbers <on/off> |
![]() <column>Filter <low>[:<high>] scoreFilter <low>[:<high>] pValueFilter qValueFilter signalFilter <column>FilterLimits <low>[:<high>] <column>FilterByRange <off/on>
|
![]() filterBy <field1:title=[+]opt1a...>
[field2:title=[+]opt2a...] |
![]() itemRgb on |
![]() maxItems <integer> |
![]() maxWindowToDraw <integer> |
![]() minGrayLevel <1-9> |
![]() noScoreFilter on |
![]() spectrum on scoreMax <integer> scoreMin <integer> |
![]() thickDrawItem <off/on> |
wig, bigWig, and bedGraph: Signal graphing tracksAnother set of common track types is one that graphs a density signal along
the genome. The graph can be a continuously varying density plot or
one that displays a density signal in only certain regions. The
oldest and simplest of these is of |
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![]() type wig <low#> <high#> type bigWig <#> <#> |
![]() type bedGraph <field> minLimit <#> maxLimit<#> |
![]() alwaysZero <off/on> |
![]() autoScale <off/on> |
![]() bigDataUrl <url/relativePath> |
![]() graphTypeDefault points |
![]() maxHeightPixels <max:default:min> |
![]() maxWindowToQuery <integer> |
![]() negateValues <on> |
![]() spanList <s1>[,s2…] |
![]() smoothingWindow <off/1-16> |
![]() transformFunc <NONE/LOG> |
![]() viewLimits <lower:upper> viewLimitsMax <lower:upper> |
![]() wigColorBy <bedTable> |
![]() windowingFunction
<mean/mean+whiskers/maximum/minimum> |
![]() yLineMark <#> yLineOnOff <off/on> gridDefault on |
![]() Examples of signal graphing tracks
|
genePred: Gene models and predictionsNOT FOR HUBS. (None of the settings in this section apply to hubs.) genePred is a variation of item-based tracks
designed especially for displaying gene
models. Gene models can be represented in |
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![]() type genePred [pepTable [mrnaTable]] |
![]() Related settings:
geneClasses <cl1 cl2...> |
![]() gClass_<xxx> <red,green,blue> |
![]() itemClassTbl <table> |
![]() itemClassNameColumn <col> |
![]() itemClassClassColumn <col> |
![]() filterBy <field1:title=[+]option1a...>
[field2:title=[+]opt2a...] |
![]() autoTranslate 0 |
![]() intronGap <#bases> |
![]() defaultLinkedTables <table1>[,table2...] |
![]() idXref <idColumn> <altIdColumn> |
![]() oldToNew <tableName> |
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. baseColorUseSequence, baseColorDefault, itemDetailsHtmlTable, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom |
![]() Examples of genePred tracks
|
bam: Compressed Sequence Alignment/Map tracksThe bam format is an indexed compressed data format for sequence alignments. It is ideal for remote access of high-throughput sequence tags and is a native output format for some high-throughput sequencing (HTS) aligners. The format of bam data is data-file pairs, with an index in a separate file. These are frequently remote datasets, not residing on the UCSC server. Please refer to the BAM track format page and the SAMtools website for information on how to create and deploy these remote data files for inclusion in the Genome Browser. |
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![]() type bam |
![]() bigDataUrl <url/relativePath> |
![]() Related settings:
bamColorMode <strand/gray/tag/off> |
![]() bamGrayMode <aliQual/baseQual/unpaired> aliQualRange <min:max> baseQualRange <min:max> |
![]() bamColorTag <XX> |
![]() noColorTag . |
![]() bamSkipPrintQualScore . |
![]() indelDoubleInsert <off/on> indelQueryInsert <off/on> indelPolyA <off/on> |
![]() minAliQual <#> |
![]() Related settings:
pairEndsByName . |
![]() pairSearchRange <#> |
![]() showNames <on/off> |
Additional settings found in the "Item or region tracks" section are also available for displaying bam tags. baseColorUseSequence, baseColorDefault, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom |
![]() Example for bam track:
|
pgSnp: Personal Genome SNP formatNOT FOR HUBS. (None of the settings in this section apply to hubs.) This format is used to display SNPs from personal genomes. It is used for the Genome Variants and Population Variants tracks. Please refer to the FAQ for information on how to prepare personal genome SNP datasets. |
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![]() type pgSnp |
![]() pgPolyphenPredTab <arg> |
![]() pgSiftPredTab <arg> |
![]() Example of a Personal Genome SNP track:
|
vcfTabix: Variant Call Format indexed by tabixVariant Call Format (VCF) is a flexible and extendable line-oriented text format developed by the 1000 Genomes Project for releases of single nucleotide variants, indels, copy number variants and structural variants discovered by the project. The format has been subsequently adopted by other large projects. When a VCF file is compressed and indexed using tabix and then made web-accessible, the Browser will fetch only the portions of the file necessary to display items in the viewed region. In other words, this is a remote data file format, as are the BAM, bigBed and bigWig formats. Please refer to the VCF and tabix track format page for a complete description of how to prepare and display VCF data. |
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![]() type vcfTabix |
![]() bigDataUrl <url/relativePath> |
![]() Related settings:
hapClusterEnabled <true|false> |
![]() hapClusterColorBy <altOnly|refAlt|base> |
![]() hapClusterTreeAngle <triangle|rectangle> |
![]() hapClusterHeight <N> |
![]() Related settings:
applyMinQual <true|false> |
![]() minQual <Q> |
![]() minFreq <F> |
Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks. maxWindowToDraw |
![]() Example of a VCF track:
|
psl: Sequence alignmentsNOT FOR HUBS. (None of the settings in this section are available for hubs, although it is likely that hub support will be added in the future.) PSL is an alignment format in which the data is typically taken from files generated by BLAT or psLayout. For further information about this format please refer to the FAQ and BLAT documentation. |
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![]() type psl <subtype> [otherDb] |
![]() blastRef <assembly.table> |
![]() colorChromDefault off |
![]() pred <assembly.table> |
![]() pslSequence <no/all/different> |
![]() transMapGene <assembly.table> transMapInfo <table> transMapSrc <assembly.table> transMapTypeDesc <label> |
![]() ucscRetroInfo |
Additional settings defined elsewhere in this document are also available for displaying psl tracks. baseColorUseSequence, baseColorDefault, chainLinearGap, chainMinScore, indelDoubleInsert, indelQueryInsert, indelPolyA, itemDetailsHtmlTable, matrix, matrixHeader, maxItems, maxWindowToDraw, showCdsAllScales, showCdsMaxZoom, showDiffBasesAllScales, showDiffBasesMaxZoom, spectrum |
![]() Examples of psl alignment tracks
|
chain and netAlign: paired species alignmentsNOT FOR HUBS. Nor are any of the settings in this section. While " Chain tracks show alignments of a "query" species to a "target" genome assembly. For example, a chimp panTro2 can be aligned to the human hg19 genome. The chain format allows for gaps in both sequences simultaneously. When chains are viewed in the Browser, they show solid boxes for alignments, separated by either single or double lines. The single lines appear when an insertion occurs in the target or a deletion occurs in the querying species. Double lines represent gaps in both species that could result from a number of causes (e.g. an inversion in one species). For more information on the "chain" format, please refer to http://genome.ucsc.edu/goldenPath/help/chain.html. A netAlign track represents the best chain for each region in the target genome. The net track will show the largest, highest scoring chains that span a region. When these chains have gaps, they may be filled in with additional chains, shown at a lower level, and gaps in these chains may in turn be filled at an even lower level. These levels help in visualizing genome rearrangements such as inversions and retroposed elements. For more information on the netAlign format, please refer to http://genome.ucsc.edu/goldenPath/help/net.html. |
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![]() type chain <otherDb> otherDb <otherDb> |
![]() type netAlign <otherDb> <otherChainTable> otherDb <otherDb> |
![]() chainColor <scheme> |
![]() chainLinearGap <loose/medium> |
![]() chainMinScore <#> |
![]() chainNormScoreAvailable <yes/no> |
![]() matrix <size> <#,#,#,#,…> matrixHeader <b1,b2,b3,b4> $matrix token in html. |
![]() spectrum on |
![]() Examples of chain and netAlign tracks
|
wigMaf: Multiple alignmentsNOT (currently) FOR HUBS. Nor are any of the settings in this section. Multiple pairwise
alignments can be displayed with " |
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![]() type wigMaf <minVal> <maxVal> |
![]() frames <table> |
![]() irows off |
![]() itemFirstCharCase noChange |
![]() pairwiseHeight <#> |
![]() speciesCodonDefault <species> |
![]() speciesDefaultOff <species1> [species2 ...] |
![]() Related settings:
speciesOrder <species1> [species2 …] |
![]() speciesGroups <sgroup1> [sgroup2 …] sGroup_<sgroupN> <species1> [species2 …] |
![]() summary <tableName> |
![]() treeImage <imageFile> |
![]() wiggle <table1> <leftLabel1>
<uiLabel1> [table2 leftLabel2 uiLabelN ...] |
![]() Examples of wigMaf tracks
|
expRatio: Microarray expression dataNOT FOR HUBS. Nor are any of the settings in this section. Though many microarray experiments have been superseded by high-throughput sequencing (e.g., ChIP-seq) experiments, several microarray tracks still exist. Further, microarray experiments can be the economical or practical choice in many instances. The datasets for the built-in microarray tracks in the Genome Browser are stored in bed 12+3 (bed 15) format that includes three additional fields: expCount, expIds, and expScores. To display correctly in the Genome Browser, microarray tracks require the setting of several attributes in the trackDb file associated with the track's genome assembly. Each microarray track set must also have an associated microarrayGroups.ra configuration file that contains additional information about the data in each of the arrays. Please refer to the microarray track section of the UCSC genomewiki for information on how to prepare microarray tracks. In particular, that document describes the format of the groupings.ra file that must be associated with an expRatio track. Note: The |
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![]() type expRatio |
![]() expDrawExons on |
![]() expScale <#> |
![]() expStep <#> |
![]() expTable <tableName> |
![]() groupings <fileName> |
![]() Example of an expRatio track:
|
snpNNN: specialized subclass of BED 6 for dbSNP variantsNOT FOR HUBS. Nor are any of the settings in this section. This particular variant of bed 6, identified by table name, is for UCSC's subset of dbSNP, NCBI's database of short genetic variants. |
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![]() type bed 6 + |
![]() chimpDb <db> |
![]() chimpMacaqueOrthoTable <table> |
![]() chimpOrangMacOrthoTable <table> |
![]() codingAnnoLabel_<table> <text> |
![]() codingAnnotations <table>[,table] |
![]() defaultGeneTracks <genesTrack>[,genesTrack] |
![]() defaultMaxWeight <1|2|3> |
![]() hapmapPhase <II|III> |
![]() macaqueDb <db> |
![]() orangDb <db> |
![]() snpExceptions <table> |
![]() snpExceptionDesc <table> |
![]() snpSeq <table> |
![]() snpSeqFile <path> |
Additional settings found in the "Item or region tracks" section are also available for displaying snp tracks. maxWindowToDraw |
![]() Example of a snp track:
|
NONE OF THESE ARE FOR HUBS. Nor are any of their settings.
altGraphX: Alternate splicing gene model tracksNOT FOR HUBS. Gene models with alternate splicing can be displayed in the Browser with this type of track. It supports no trackDb settings beyond the common ones. |
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![]() type altGraphX |
![]() Example of an altGraphX track:
|
bedDetail: Text extended bed trackNOT FOR HUBS. This is an extension of BED format. BED detail uses the first 4 to 12 columns of BED format, plus 2 additional fields that are used to enhance the track details pages. The first additional field is an ID, which can be used in place of the name field for creating links from the details pages. The second additional field is a description of the item, which can be a long description and can consist of html, including tables and lists. |
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![]() type bedDetail <#> |
Additional settings defined elsewhere in this document are also available for displaying bedDetail tracks. itemRgb, url, urlLabelTODO: Currently almost no settings or configuration options are supported by bedDetail tracks. However, there is very little, in principle, that should prevent adding support for almost all the "Item or region tracks" settings. |
![]() Example of a bedDetail track:
|
clonePos: Genome coverage tracksNOT FOR HUBS. This is a specialized format track that is only used for showing the coverage in the human genome. It supports no trackDb settings beyond the common ones. |
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![]() type clonePos |
![]() Example of a clonePos track:
|
ctgPos: Physical map contigs tracksNOT FOR HUBS. This is a specialized format track that is used for "physical map contigs" on the human genome. It supports no trackDb settings beyond the common ones. |
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![]() type ctgPos |
![]() Example of a ctgPos track:
|
rmsk: Repeat masking tracksNOT FOR HUBS. This is a specialized format track that is used only for the repeat-masking track. For completeness it is being briefly described here. These tracks are created created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
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![]() type rmsk |
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. maxWindowToDraw, spectrum |
![]() Example of a Repeat Masking track:
|
snake: Self referencing alignment tracks - EXPERIMENTALNOT FOR HUBS. This is a specialized format track that shows the snaking course of bi-directional and overlapping alignments. This format can help illustrate inversion-type rearrangements that align to the plus strand, then the minus strand, and again to the plus strand. It can also be used to illustrate overlapping alignments, such as when a duplication has occurred compared to the reference genome. |
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![]() type snake <db> otherDb <otherDb> |
Additional settings found in the "Item or region tracks" section are also available for displaying snake tracks. maxWindowToDraw, spectrum |
![]() Example of a snake track:
|
All tracks have to be assigned to one predefined track group ("Mapping and sequencing",
"Genes", etc).
In addition and depending on how closely related they are, tracks can be organized into one of three
hierarchical containers:
Predefined major track groupingsNOT FOR HUBS. The simplest grouping: |
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![]() group <groupId> |
![]() Example of a track belonging to a predefined group:
|
Supertrack settingsThe first hierarchical container is called the supertrack, which may be thought of as a folder that holds other tracks. The Browser currently supports only one level of supertrack folders. Generally the subtracks of a supertrack are of differing types. If all the children are of the same type, it is often better to use the "compositeTrack" grouping described below. If all of the children are wig or bigWig tracks, it may be of interest to use a signal overlay "container multiWig" grouping. Signal overlay tracks display the signal data from several subtracks as colored transparencies, making it possible to see the data of several tracks together in a condensed view. See the multiWig section for more information. Supertracks can contain composite tracks and container multiWigs, but not vice versa. With supertracks, composite tracks, and container multiWigs, children will inherit the settings from their parents, but can override their parent settings within their own stanzas. |
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![]() superTrack on |
![]() parent <superTrack> |
![]() Example of a Supertrack:
|
Composite TracksComposite tracks are
another level of hierarchy and are meant to group very similar tracks
(called "subtracks") together such that they can all
share the same configuration settings. In its simplest form a
composite holds tracks all of the same type (such as bigBed).
Initially, all track within the set are configured identically.
Usually only some of the subtracks are visible by default, and these
will have the same display mode (e.g., Currently only the following track types can be organized into a composite: item-based tracks (bed, bigBeg, broadPeaks, etc.), signal-based tracks (wig, bigWig, etc.), other remote file-based tracks (bams, vcf, etc.), chains/nets, genePred, psl, and wigMaf-type tracks. |
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![]() compositeTrack on |
![]() parent <composite> [off/on] |
![]() allButtonPair on |
![]() centerLabelsDense <off/on> |
![]() dragAndDrop subTracks |
![]() Example of a Composite track:
|
axt – rare bed 3 variant (replaced with netAlign?), panTro1.axtNetHg16
drosophila/dp1/trackDb.ra:type axt dm1
human/hg13/trackDb.ra:type axt mm3
human/hg15/trackDb.ra:type axt mm3
worm/ce1/trackDb.ra:type axt cb1
worm/ce2/trackDb.ra:type axt cb1
bedLogR – encode 1% test only??? Not found with tdbQuery from *
human/encodeTest/wgEncodeMetaCheckTest.ra
chromGraph - ??? Not found in tdbQuery -strict from *
gff http://genome.ucsc.edu/FAQ/FAQformat.html#format3
Not found in tdbQuery -strict from *
gtf http://genome.ucsc.edu/FAQ/FAQformat.html#format4
Not found in tdbQuery -strict from *
maf – replaced by wigMaf hg17, tdbQuery -strict: 1 track: fr1.tbaFishBirdCFTR
http://genome.ucsc.edu/FAQ/FAQformat.html#format5
net but not netAlign - custom only??? Not found with tdbQuery non strict
sample – RARE bed variant, hg15.affyTranscriptome, Affymetrix Transcriptome
hg15.hg15Mm3L
Completely replaced by type wig and more recently bigWig
Rejected settings | For Types | Reason |
---|---|---|
accession |
all ENCODE only | ENCODE only; DEPRCATED (replaced with mdb ) |
canPack <off/on> |
all | NOT FOR HUBS. Deprecated.
Almost tracks can be displayed in the five
standard visibilities. However on some track types such as
wiggles, Example: canPack on |
cdsDrawDefault | genePred | There are a number of occurrences of cdsDrawDefault in our trackDbs, always set to ‘genomic\ codons ‘. However, I have found no documentation and no code that references this setting. |
cdsDrawOptions | psl | I have found no documentation and no code that references this setting. Also, I do not see it in our trackDbs. |
cdsEvidence |
genePred | Used by JK experimental tracks only as either
jkgTxCdsEvidence or jkgTxCdsEvidence2 .
This will show an evidence table named in the setting.
|
cell |
bed, bedGraph ENCODE only | Obsolete: replaced with metaDb. |
chip |
expRatio, bed ENCODE only | DROP (no takers in any of our trackDb.ra files) |
dateSubmitted |
bedGraph, bed ENCODE only | Obsolete: replaced with metaDb. |
dateUnrestricted |
bed ENCODE only | Obsolete: replaced with metaDb. |
db |
chain, netAlign, genePred, bed 3 | Not found in any of our trackDb.ras. Further, this is the same as assembly so implicit. |
dbProfile | all | In hg18 experimental and cancerGenomics only. |
dividers |
all | OBSOLETE: use sortOrder instead. |
endFudge | bed | Special case for hg17 HGSV Discordant (variation) tracks. Used in hgc to fudge chromEnd, I think. |
ensArchive | genePred | Only in danRer4 Ensembl NonCoding to generate an Ensembl URL. |
ensemblTranscriptIdUrl |
genePred ENCODE Gencode Only | Special for ENCODE Gencode to generate external URL. |
ensemblGeneIdUrl |
genePred ENCODE Gencode Only | Special for ENCODE Gencode to generate external URL. |
ensemblIdUrl |
genePred ENCODE Gencode Only | Special for ENCODE Gencode to generate external URL. |
expProbeTable |
expRatio | Can't find code that supports this.Rare: only in human. affyHumanExon "Affy All Exon" |
extTable | all | This setting points to a one record table that holds the external filename. This
should be replaced by:
track,
table or
bigDataUrl.
(rare bigWig hg18.brTestPlus experimental track) |
extraFields | bed | OBSOLETE: replaced by looking up "as" table
description. However, that method does not allow for:
|
filePos | all | Can't find this in any of our trackDb.ra files. |
filterTopScorers |
bed5FloatScoreWithFdr, bed5FloatScore ENCODE only | Currently only used by pilot encode 1%.
Presents user option to limit to the top scoring N items. Might be useful in other MySQL table based tracks but how valuable is it? |
gainColor lossColor |
bed ENCODE only | Currently only used by pilot encode 1% in hg17.encodeDless.
Provides special color for "gain" and "loss" items. |
graphType |
bedGraph | Not found in code. Probably typo of graphTypeDefault. (rare hg18.encodeRegulomeDnaseArray) |
hgGene | genePred | Cannot find code for this. No effect. ??? |
informant | genePred | Special setting for N-SCAN genes. Swapped into html description page. |
inputTracksSubgroupDisplay |
bed, factorSource ENCODE only | Only in hg18/hg19 wgEncodeReg*Clustered tracks. In code #ifdef TO_BE_REMOVED. |
itemAttrTbl | genePred | Only used in borEut13. transMapRefGene. |
linesAt | chromGraph | Unused track type (tdbQuery -strict). |
longlabel | genePred | Typo, should be longLabel. |
longLabelClip |
all | Only used in sacCer3 (tdbQuery -strict). |
mafDot | wigMaf | Can't find this in any of our trackDb.ra files and only supported as cart var. |
mafDotDefault |
wigMaf | Can't find this in any of our trackDb.ra files. |
mapDispatcher |
expRatio | Only hg17 group "x" [tingwang 2007] and not in C. |
maxScore | broadPeak | Obsolete, replaced with scoreFilterLimits. |
metadata |
all ENCODE only | OBSOLETE: replaced by metaDb. Currently only way for datHubs to have metadata dropdowns. Used by WashU hubs. |
mgiUrl | bed | Special case variant of url used by no current tracks (tdbQuery -strict). |
mgiUrlLabel | bed | Special case variant of url used by no current tracks (tdbQuery -strict). |
minMax | chromGraph | Unused track type (tdbQuery -strict). |
minScore |
bed, narrowPeak, broadPeak | Obsolete, replaced with scoreFilterLimits. |
msaTable |
wig, wigMafProt, wigMaf | Only hiv tracks use this. Code in wigMaf display and is used to look up species order. |
ncbiAccXref | bed | Special case used by hg17/hg18 kiddEichler tracks. Names a table to convert kiddEichler IDs to NCBI IDs and print links. |
nextItemButton |
all | This setting lets you override the Browser wide setting to disable nextItem arrows (which is off by default). When this is on, the nextItem arrows will show up for your track. The opposite does not seem to be the case, where nextItems are enabled, but you want to exclude them from your track. |
noInherit | all | This one should be
OBSOLETE but there continue to be edge cases where this setting
has some affect. Currently only 2 places this is read this:
|
nonBedFieldsLabel |
bigBed | OBSOLETE when bigBed has "as" definitions. Instead, the extraFieldsPrint should pick up the non-standard bed fields straight from the as definition. |
notNCBI | bed | Only used in drosophila dm2/dm3. Referenced in hgc.c code. |
ococci | bed | Not referenced in any of our trackDb.ra files or in code. |
otherOrg | chain, netAlign | Typo: should be otherDb. |
onlyVisibility |
all | Not universally supported (rightClick/subtrack
cfg, etc.) so deprecate or else expand. This setting restricts
the visibility options of a track to only one setting such as
"full ". (rare hg19.lincRNAsAllCellTypeTopView)
|
otherDbTable | bed | Special case for Jackson lab's QTL (Quantitative Trait Locus) tracks. |
pairedEndUrlFormat | bed | Special case only used on kiddEichler track. This is another external URL variant. |
pairwise | wigMaf | Deprecate, replaced by summary. |
patDb | expRatio | Only hg17 group "x" [jzhu 2007] and not referenced in C. |
patKey | expRatio | Only hg17 group "x" [jzhu 2007] and not referenced in C. |
patTable | expRatio | Only hg17 group "x" [jzhu 2007] and not referenced in C. |
pgDbLink | bed | Special only used
in hg18/hg19 Genome Variants so far.
This setting is used to name one or more tables that hold links to phenotype and other databases for pgSnps. Each table must have chrom, chromStart, chromStop, name and srcUrl as fields. The links will be seen in the bed item details page and will be looked up in each listed table by item location. Example: pgDbLink pgKb1PhenCode pgKb1Snpedia pgKb1Hgmd |
private | bed | Only used in human/hg7/trackDb.ra, and not even there using tdbQuery -strict. Prevents access to data by removing from trackList when doing "pruneEmpties". Gotta wonder when the track is ever seen in the browser or why it is a track at all. |
pslTable | bed | Special for hg18/hg19 illuminaProbes "Illumina
WG-6". Used in hgc. (Hardwired to be the same
illuminaProbesAlign when track is
"illuminaProbesAlign".) Used for making an hgcAnchor
htcIlluminaProbesAlign .
|
pubsArticleTable |
bed, psl | Special for publications track. |
pubsMarkerTable | bed, psl | Special for publications track. |
pubsPslTrack |
bed, psl | Special for publications track. |
pubsSequenceTable | bed, psl | Special for publications track. |
refSeqAnnoVersion | genePred | Special for rheMac2.refSeqAnno track. Not found in code. |
scoreFilterMax |
bed, bedLogR, peptideMapping, bigBed | OBSOLETE: replaced by scoreFilterLimits |
searchMethod |
bed | Error. Should be part of searchTable stanza, not track stanza.
TODO: Document searchTable stanza. |
searchType | bed | Error. Should be part of searchTable stanza, not track stanza.
TODO: Document searchTable stanza. |
selectSubject |
psl | Special only used in hiv(only used by hiv and h1n1. (Just h1n1 according to tdbQuery -strict). |
seqTable | bed | Special for hg18/hg19 illuminaProbes "Illumina
WG-6". Used in hgc. (Hardwired to be the same
illuminaProbesSeq when track is
"illuminaProbesAlign".) Used for making an hgcAnchor
htcIlluminaProbesAlign .
|
settingsByView |
all | OBSOLETE: replaced with "view in the middle" view as separate track. |
snpTable <table> |
bed gwasCatalog only | Special for gwasCatalog: table used to map dbSNP IDs to genomic coords |
snpVersion |
bed gwasCatalog only | Special for gwasCatalog: dbSNP build number of table used to map dbSNP IDs to genomic coords |
speciesTarget |
wigMaf | OBSOLETE. Not in our trackDbs (tdbQuery -strict).
Specifically ifdef'd out of code with
#define BRANEY_SAYS_USETARG_IS_OBSOLETE.
|
speciesTree | wigMaf | OBSOLETE. Replaced by treeImage.
Not in our trackDbs (tdbQuery -strict).
Specifically ifdef'd out of code with
#define BRANEY_SAYS_USETARG_IS_OBSOLETE.
|
speciesUseFile <fileName> |
wigMaf |
Deprecated Much more rarely used, this setting can
replace Example: speciesUseFile speciesLists/conserved8Way.txt |
stripPrefix | bam | Not yet implemented? Only on hg18.oneKGHighCovSeq experimental track. |
subgroups | bed | Typo: should be subGroups. |
subTrack | all | OBSOLETE: replaced with parent. |
symbolTable |
bed, genePred | In hgTracks, flyBaseGeneName() methods, if an item name is found in this symbol table, the symbol name will be shown instead. Found in drosophila and strangely rn4 RGD Genes (but table named in rn4 does not have a symbol column. Instead, symbol lookup is hard-coded to rgdGene2ToSymbol). |
txInfo | genePred | Only seems to be used in experimental tracks in hg18 and mm8. |
urlName | genePred | Not referenced in code and rarely used. (e.g. hg18: encodePseudogeneConsensus, encodePseudogeneYale). |
url2 | bed | Special cased second URL used much like url. |
url2Label | bed | Special cased second URL label used much like urlLabel. |
useScore | bed, factorSource, bed5FloatScore, broadPeak | Deprecate: replaced with spectrum as a slighly less obscurely named setting. |
vegaGeneIdUrl |
genePred ENCODE Gencode Only | Special for ENCODE Gencode to generate external URL. |
vegaTranscriptIdUrl |
genePred ENCODE Gencode Only | Special for ENCODE Gencode to generate external URL. |
visibilityViewDefaults | all | OBSOLETE since view in the middle change. LOSE |
wgEncodeGencodeVersion |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeAttrs |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeExonSupport |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeGeneSource |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeTranscriptSource |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodePdb |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodePubMed |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeRefSeq |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeTag |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeTranscriptSupport |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeUniProt |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodePolyAFeature |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeAnnotationRemark |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
wgEncodeGencodeTranscriptionSupportLevel |
genePred ENCODE Gencode Only | Special for ENCODE Gencode. |
yLinOnOff | wigMaf |
Typo: should be yLineOnOff. |
yalePseudoAssoc |
all ENCODE Gencode Only | Special for ENCODE Gencode. |
yalePseudoUrl |
all ENCODE Gencode Only | Special for ENCODE Gencode to generate external URL. |
yaleUrl |
all ENCODE Gencode Only | Special for ENCODE Gencode to generate external URL. |
track
Required: Yes
This is the name of
the dataset and must be unique within the Genome Browser or
dataHub. Typically this is the MySQL table name or remote data
file root name (without path or suffix). Must begin with a letter
and contain only the following chars:
[a-zA-Z0-9_
].
Example:
track myFirstTrack
type
Required: Yes
Declares the format of the data and is used to determine display methods and options.
Valid settings:
altGraphX, bam, bed, bed5FloatScore, bedGraph, bedRnaElements, bigBed, bigPsl, bigChain, bigMaf, bigWig, broadPeak, chain, clonePos, coloredExon, ctgPos, downloadsOnly, encodeFiveC, expRatio, factorSource, genePred, gvf, ld2, narrowPeak, netAlign, peptideMapping, psl, rmsk, snake, vcfTabix, wig, wigMaf
Detailed descriptions of each type can be found below. In many cases the type setting includes additional parameters to further specify the data format. Some track types have additional setting requirements, to be discussed below.
Example:
type bed 6 +
type
Required: Yes
Declares the format of the data and is used to determine display methods and options.
Valid settings:
bam, bigBed, bigWig, vcfTabix,
Detailed descriptions of each type can be found below. In many cases the type setting includes additional parameters to further specify the data format. Some track types have additional setting requirements, to be discussed below.
Example:
type bigBed 6 +
shortLabel
Required: Yes
Specifies the track's "short label", which is used in a number of places in the Browser to identify the track. For example, the short label is displayed alongside the track in the Browser image. This label must be brief and is limited to 17 printable characters.
Example:
shortLabel Human mRNAs
longLabel
Required: Yes
Specifies the track's "long label", which is also used in numerous places in the Browser to identify a track. For instance, the long label is displayed above the track's data in the Browser image. This label should be descriptive enough to allow users to uniquely identify the track within the Browser. It is limited to 76 printable characters.
Example:
longLabel Human mRNAs from GenBank
visibility
Required: No
Visibility (i.e. "display mode") specifies which of 5 modes (including 'hide') should be used to display the track within the Browser image. This setting is almost always dynamically customizable by each user. The exact configuration of the display for each mode depends upon the track's type, and some modes may not be supported for certain track types. Please note visibility settings in composite subtracks are directly inherited from the parent. Therefore, any visibility lines added at the subtrack level of a composite will be ignored. Be sure to experiment with this setting to verify that it works as expected for your track type and track structure.
Valid settings:
hide
: DEFAULT. The track is not displayed in the Browser image unless
the user changes the display setting.dense
: The track is displayed as a single line or
ribbon. In many cases multiple items are summarized or drawn on top of
one another, and the long labels are not displayed.squish
: Each item is drawn individually, but at half height
and without a label. (Not supported for all types.)pack
: Items are displayed individually at full height, but
in a much more compact vertical space than in full mode.
(Not supported for all types.)full
: Each item is displayed as a separate line in the
Browser image. Graphed signals may be displayed in varying heights.Example:
visibility dense
html
Required: No
Specifies a file that contains the complete description of a track in HTML format. The path of this file name is relative to the path of the trackDb file. The ".html" suffix is implied.
To be consistent with standard Genome Browser track descriptions, this description should contain several sections as seen below. Here is a link to an example template that you can use.
Description
A few sentences describing the contents of the track and what it attempts to show. The description can include additional paragraphs giving further details and can include links to outside sources.
Display Conventions and Configuration
A description of what the display represents. This includes a description of conventions for coloring and any special glyphs used in the track. It may describe how to interpret scores or full signal values. This section can also be used to describe how to customize the display by using configuration controls.
Methods
A description of how the data was generated, which may include how physical samples were treated as well as explanations of data-handling algorithms.
Credits
Names and institutions of those who performed the experiments and/or prepared the data as well as any funding sources. This section should include a contact email address for questions concerning the data.
References
References to any published work referring to or dependent upon this data as well as any sources upon which the work is based or can be understood.
Example:
html docs/myFirstTrack
bigDataUrl <url/relativePath>
Required: For Hubs
The location of a remote data file containing the bulk of the data for the track. This setting is required for all data tracks in a track hub. It is currently not supported for local tracks.
The setting is either the full URL (including http:
or another protocol)
or it is relative to the directory in which the trackDb file containing this setting
is located. The file must be in one of
the supported remote data file formats: bam, bigBed, bigWig or
vcfTabix. Note that bam and vcfTabix types require a separate
index file that must have the same name as the data file plus a
standard suffix (".bai" and ".tbi" respectively).
Example:
bigDataUrl http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bbor
bigDataUrl biBrainH3K4me1.bb
boxedCfg <on/off>
Configuration controls can be placed inside a box on the configuration page. This setting is decorative only, but can make a busy page look more cohesive. Not all track types currently support this feature, but the most common types do, including wig, bigWig, bed, and bigBed. DEFAULT: off.
Example:
boxedCfg on
canPack <off/on>
NOT FOR HUBS. Deprecated.
Most tracks can be displayed in all five
visibilities modes. However on some track types such as
wiggles, the squish
and pack
modes offer no real advantage
over the dense
and full
modes. By default, these tracks will
not offer the squish
and pack
vilibility settings.
Nevertheless, you can make your track offer
these visibilility choices by turning canPack on. Note: subtracks
of composites will always offer all five choices.
Example:
canPack on
color <red,green,blue>
Many track types allow the color of the data displayed in the image to be specified with this setting. The setting accepts red, green and blue values, each in the range of 0-255 and delimited by commas. Though this setting is widely supported, some track types in certain display modes ignore it, such as the EST tracks in dense mode.
Example:
color 255,0,0
This example sets the color to red.
altColor <red,green,blue>
Many track types allow setting a color range that varies from color
to
altColor
. For instance the CpG Island tracks use the altColor
setting to display the weaker islands, while the stronger ones are rendered in
color
. If altColor
is not specified, the system will
use a color halfway between that specified in the color
tag
and white instead.
Example:
altColor 0,0,255
This example sets the alternate color to blue.
chromosomes <chr1,chr2,...>
Some datasets do not contain data for all chromosomes of a genome. When this is true, use this setting as a comma-separated list of the chromosomes that are covered. The system displays a message that no data is available when the user browses chromosomes not included in this list.
Example:
chromosomes chr1,chr7,chr18,chr19,chr22,chrX,chrM
configureByPopup <on/off>
NOT FOR HUBS.
Most track displays that can be configured by a user can also be configured from directly within the Browser image through a right-click option that pops up a configuration dialog. While this functionality works on the majority of track types, some configuration dialogs are too complex or have too much embedded javascript control to be reliably configured through a pop-up. To turn off the ability to configure the track via right-click, change this setting to "off". The user will still be able to configure the track on the track's configuration page. DEFAULT: on.
Example:
configureByPopup off
dataVersion <str>
Many tracks undergo multiple revisions over time. In some cases, the older versions should be retained, but even if they are not, it can be useful to declare the current version of the track. Use this setting to display a version statement on the track configuration page and item details page of a track. The string will support limited HTML.
Example:
dataVersion May 2011 <em>beta</em>
directUrl <url>
By default, items shown in the Browser image can be linked to a details page giving information about that item. The link can instead go to the URL declared here. The URL is formatted as a printf line including the following fields in this order:
Not all fields need be present, but those present must be in this order, and if a later field is present, all earlier fields must be used. The URL can either be a full external URL or local to the web site.
Examples:
directUrl http://mygenes.org/cgi-bin/geneView/%sor
directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s
hgsid on
NOT FOR HUBS.
The "cart" is a hidden table that contains the persistent selections that users have made in the Genome Browser. To ensure your directUrl has access to these cart settings, include the user's Browser ID with this setting.
directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s hgsid on
In this example the URL specified by directUrl
will have the user's
Browser ID appended so that cart settings will be available.
iframeUrl <url>
This setting allows integrating an external html page into the default details page, as an iframe. The usual replacement variables can be used within this URL:
name
of an item or other string id depending upon the fields in the
given track's type.The URL can either be a full external URL or local to the web site.
In HTML, iframes cannot be resized easily, so the default static size is 1024 pixels. This can be changed with iframeOptions
Examples:
iframeUrl http://www.ncbi.nlm.nih.gov/nuccore/$$ iframeOptions height='600' width='1024'
iframeOptions <string>
When iframeUrl is used, this statement specifies a string that is inserted literally into the HTML <iframe> tag. It can include options needed for iframe formatting, like width, height, scrolling, etc.
If the statement is not present, the default is width='100%' height='1024'
.
Note: dynamic resizing of iframes is not trivial, as they have to be resized with javascript, across domains. We recommend keeping the size static and to use scrollbars. If dynamic resizing is required, the iframed page has to include a few lines of special HTML and javascript code and one has to modify its body-tag, like this (see stackoverflow):
... html header ... <body onload="iframeResizePipe()"> <iframe id="helpframe" src='' height='0' width='0' frameborder='0'></iframe> <script type="text/javascript"> function iframeResizePipe() { var height = document.body.scrollHeight; var pipe = document.getElementById('helpframe'); pipe.src = 'http://genome.ucsc.edu/inc/iframeHelper.html?height='+height+'&cacheb='+Math.random(); } </script> ... rest of webpage ...
Example:
iframeOptions width='800' height='800' scrolling='yes'
This example fixes the size to 800x800 pixels and activates scrollbars.
directUrl <url>
By default, items shown in the Browser image can be linked to a details page giving information about that item. The link can instead go to the URL declared here. The URL is formatted as a printf line including the following fields in this order:
Not all fields need be present, but those present must be in this order, and if a later field is present, all earlier fields must be used. The URL can either be a full external URL or local to the web site.
Example:
directUrl http://mygenes.org/cgi-bin/geneView/%s
otherDb <otherDb>
Track types that show pairwise alignments often need to declare the other species/assembly included in the alignment. Types that use this setting include bed, chain, netAlign, psl and snake.
Example:
otherDb mm10
This example sets the second assembly in the alignment to the mouse mm10 assembly.
origAssembly <db>
NOT FOR HUBS.
The original assembly version for which the dataset was generated. Datasets generated by mapping to one genome assembly may prove useful enough to map to a more recent assembly. Ideally datasets will be regenerated to map to the new assemblies coordinates, but sometimes this is not practical or expedient. Therefore, the dataset may have its genome coordinates "lifted over" to the more recent assembly. In some cases this results in an inferior but nevertheless useful representation. Such datasets should have their original assembly defined with this setting.
Example:
origAssembly hg18
pennantIcon <icon> [html [tip]]
Certain tracks can be visually flagged in the Browser by use of an icon and a link to a description of the icon's meaning. The icon is displayed next to the track's short label in the track groups section below the Browser image, and on the track's description and configuration pages. This setting has three parts:
Example:
pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18"
priority <float>
The priority is used to define the order of a track within its track group or data hub, as well as its default order within the Browser image. The order within the image can be dynamically changed by the user and will always depend upon which other tracks are currently visible. Typically the priority is set only for tracks that are on by default in order to move them ahead of other tracks. Prioritized tracks within a group or data hub are displayed in ascending priority order, followed by unprioritized tracks sorted alphabetically by short label. Tracks of the same priority within a group or hub are sorted by short label. Priority is a floating point number. Default: 0.
Example:
priority 50
release <alpha/beta/public>[,beta/public]
NOT FOR HUBS.
This specifies the version of the Browser where the track will be displayed. It can contain any combination of the three values:
Default: alpha,beta,public (all three Browsers).
Example:
release alpha,beta
table <tableName>
NOT FOR HUBS.
The track setting of most tracks is the same as
the table name. However, in some cases it is desirable to
reference the same table in more than one track.
An example of this is showing a table as a single signal track and
as part of a combination overlay track, as described later in this
document. For data contained in MySQL tables, this setting must be used
if the track
setting is not the name of the table.
Example:
track mySecondTrack table myFirstTable
tableBrowser <off/on> [table1 ...]
NOT FOR HUBS.
The Table Browser typically allows querying and downloading of some or all of the raw data for a track. This setting can be used to block Table Browser access to datasets with restrictions (for example, those with confidentiality or licensing limitations). By naming additional tables in this setting, access to those tables can be denied as well.
Example:
tableBrowser off decipherRaw knownToDecipher
The table for this track, as well as the decipherRaw and knownToDecipher tables, are blocked from Table Browser access.
url <url>
urlLabel <label>
idInUrlSql <sql for id>
Many tracks allow an external link when an individual track data item is examined. Use this setting to put a link to an external URL on the details page. The url may include wildcards that will be substituted with values from the track data or other Browser variables:
name
of an item or other string id depending upon the fields in the
given track's type.The default prompt the user will see for this url is "outside link:". Use
urlLabel
to provide a more informative prompt.
For local (non-hub) tracks, an additional setting can be used to find an ID
from another table based upon the item name or id from the track's
table. The value found will replace the "$$
" token in the url
.
Note that the format of this trackDb setting is a normal C
language format so that the item will replace the "%s"
token in the sql statement.
Example:
url http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$ urlLabel NCBI Details: idInUrlSql select name from sibTxGraph where id=%s
url <url>
urlLabel <label>
Many tracks allow an external link when an individual track data item is examined. Use this setting to put a link to an external URL on the details page. The url may include wildcards that will be substituted with values from the track data or other Browser variables:
name
of an item or other string id depending upon the fields in the
given track's type.The default prompt the user will see for this url is "outside link:". Use
urlLabel
to provide a more informative prompt.
Example:
url http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$ urlLabel NCBI Details:
urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...
This is similar to the url tag, but allows urls on fields that are not the "name" field. Use this statement if you need multiple linkouts on the details page or if your linkout is not based on the name field.
Put the identifiers for these links into extended bigBed fields as explained in example 3 of the bigBed documentation. The field names from your .as file are the field names referenced in this statement. The urls in this statement support the same wildcards as the url statement. Make sure to enclose the URLs in double quotes. The default label for the identifier is the field description in the .as file (all text after the # mark).
If the field contains a "|" symbol, the part before the symbol is used to replace the $$ wildcard and the part after it as the label. This is similar to how Wikpedia markup encodes links. In the example below, a value for the field pmid of "115330|Doe, J. et al" would create a link with the URL http://www.ncbi.nlm.nih.gov/pubmed/115330 and the label "Doe, J. et al" .
Example:
urls pmid="http://www.ncbi.nlm.nih.gov/pubmed/$$" spId="http://www.uniprot.org/uniprot/$$"
skipEmptyFields on
If this setting is "on", the item details page will not show fields that have empty values. This can be useful when you have numerous extra fields but only few of them have a value.
skipFields <fieldName1>="<url1>" <fieldName2>="<url2>" ...
This setting can be used to suppress extra fields on the item details page. It can be useful if you do not want to show fields that are only used for mouseOvers or labels.
Example:
skipFields mouseOver,labelField,hiddenField
sepFields <fieldName1>="<url1>" <fieldName2>="<url2>" ...
This setting changes the item details page and splits the table used for showing extra fields before any of the specified fields. It can be useful to visually separate extra fields into logical categories.
Example:
sepFields pmid,spId
mouseOverField <fieldName1>
For bigBed files with more than 8 fields, this adds mouse over text that are different from the "name" field of a bigBed file. If the field is empty then the mouse over will fallback to the name field.
To make this work, create a bigBed file with at least 8 columns and put the text for the mouse over into extended an bigBed field as explained in example 3 of the bigBed documentation. The field name from your .as file is the field name referenced in this statement.
Example:
mouseOverField comment
wgEncode on
NOT FOR HUBS.
This setting designates an ENCODE track. It activates the following special features:
Example:
wgEncode on
Some of the most common track types are those that highlight regions or items of varying size in a genome assembly. There are many variations to the "items" track, most of which can be represented with a bigBed format. This format is really a cluster of many formats all starting with three common fields (chromosome start end) and having optionally many more fields. For complete bigBed format definitions please see the bigBed help page.
type bed <3-12> [+/.]
type bigBed <3-12> [+/.]
Both bed and bigBed
declare the number of standard bed fields in the data.
Additional fields may follow these standard ones. If so, the
type should end with a '+
' (plus). Even if there are not
additional non-standard fields, the additional parameter '.
' (dot)
is needed, if this track is meant to be configurable.
Examples can be found below.
type bigBed <3-12> [+/.]
Type bigBed declares the number of standard "bed" fields in the data.
There may be additional fields following these standard ones. If so, the
type should end with a '+
' (plus). Even if there are no
additional non-standard fields, the parameter '.
' (dot)
must be specified if this track is meant to be configurable.
Examples can be found below.
type bed5FloatScore
type bedRnaElements
type broadPeak
type coloredExon
type gvf
type ld2
type narrowPeak
type peptideMapping
Each of these is a specialized variation of the bed format. Their specialized definitions should be sought elsewhere. However, these item tracks share many of the same configuration options available to bed tracks.
An example can be found below.
bigDataUrl <url/relativePath>
This setting is for remote data file type tracks (e.g. bigWig) and is fully described in the "Common trackDb settings" portion of this document.
colorByStrand <red,green,blue> <red,green,blue>
To color items
differently by the strand they align to, use the colorByStrand
setting. The first color will be used for plus strand alignments
and the second for the minus strand. This setting is incompatible with spectrum
and all items on the same strand will have the same color, regardless of the item's
score.
Example:
colorByStrand 255,0,0 0,0,255
Plus strand alignments will be colored red, and minus
strand alignments will be blue. This setting is incompatible with spectrum
,
and therefore all items on the same strand will have the same color, regardless of the item's
score.
compareGenomeLinks <db[.table[.column]]=label>
[db[.table[.column] =label …]
NOT FOR HUBS
Sometimes the
features that a bed track highlights in one genome are also
displayed in tracks of other genomes. If an item of the same name
exists in the bed tracks of two or more genomes, a bridge can be
readily made between them through links on the item's detail page. To establish
this association, the feature must have the same name in each genome, and the name
must be unique within the bed track of each genome. The components of this
setting are a genome assembly database, an optional table and column,
with a label for the link. If the column parameter is omitted, it is
assumed to be name
. If the table is omitted, it
is assumed to be the same as the current table. Links to multiple
genomes can be established with this setting, as each pair is
joined by '=
' and delimited by space. Be sure to use
'_
' as a substitute for spaces in the labels.
Example:
compareGenomeLinks panTro2=Chimpanzee_(March_2006) rheMac2=Rhesus_(January_2006) \
mm9=Mouse_(July_2007) rn4=Rat_(November_2004) canFam2=Dog_(May_05) \
bosTau4=Cow_(October_2007)
In this example for
the hg18 ENCODE bi-directional promoter track, each genome has a
track of the same name, and the names are unique within each track.
However, a named bi-directional promoter will not be found in
every genome; therefore, only links to genomes where the name is actually
found will be displayed.
denseCoverage <maxVal>
bigBed specific
Type bigBed tracks
in dense mode do a density plot based on maximum coverage seen at
each pixel. The maxVal corresponds to the count at which the plot
reaches maximum darkness. If maxVal is 0 then this will be
calculated from the data itself.
Example:
denseCoverage 100
labelOnFeature <on/off>
Usually, labels (the BED name field) are drawn next to the
features. This statement tries to draw the feature
label over the exon blocks. The effect depends on the size of the feature
on the screen, which in turn depends on the zoom level. If there is not enough
space for 4 characters, no label is drawn at all. If there is more space,
the label is drawn with a contrasting color onto the exon-like blocks.
If they are too short for the text, it is trimmed to fit into the available space
and the suffix "..." appended. Note that features should not have too
long thin (UTR) regions, as the text might be hard to read
in these parts.
To keep the text readable, the arrows that indicate the strand are shown over
introns, but suppressed on blocks, so the statement should be used
for tracks where strand is not of primary importance, not defined in the
BED strand field or deactivated
with exonArrows.
Example:
labelOnFeature on
exonArrows <on/off>
On tracks that show
exons or blocks within features, exon arrows allow the user to jump to
the next exon or block outside the image. Exon arrows are typically shown by default
in these types of tracks, with the exception of tracks in the Regulation group.
The arrows can be explicitly shown or hidden using this setting.
Example:
exonArrows off
exonNumbers <on/off>
On tracks that show
exons or blocks within features, mouseover/hover shows exon and intron numbers.
Exon and intron numbers are typically shown by default
in these types of tracks.
The mouseover exon and intron numbers can be explicitly shown or hidden using this setting.
Example:
exonNumbers off
<column>Filter <low>[:<high>]
scoreFilter <low>[:<high>]
pValueFilter
qValueFilter
signalFilter
<column>FilterLimits <low>[:<high>]
<column>FilterByRange <off/on>
NOT FOR HUBS. Not yet supported by bigBeds
A number of
numerical filters are available for bed tracks. These are
conveniently named by the field that is filtered on. The most
common numerical filter is based on the standard bed field
score
, and is thus controlled by the scoreFilter
setting. Other examples are pValueFilter, qValueFilter and
signalFilter, which are filters on non-standard bed fields defined
in the broadPeak and narrowPeak formats. These numerical filter
settings should include the default value. If the numeric field
is floating point, the default should contain at least one decimal
place.
By default the range
of values for a numeric filter is 0 to 1000. However, you
can explicitly set the upper and lower limits of the filter by
setting <column>FilterLimits
.
The numeric filters
will exclude items that fall below the setting. That is, a
scoreFilter of 800 will exclude all items with a score below 800.
You can also filter for values within a range, by including the
<column>FilterByRange
setting. For example, a
scoreFilter
range of
800-900 will include only items with scores at or above 800 and
below 900.
Note: multiple
filters of different fields are allowed.
Examples:
scoreFilter 100
In this example, the standard bed
field score
, which is an integer, will be used to filter items
in the track. By default, items with scores below 100 will be
excluded. Also by default the limits of the scoreFilter are
0-1000.
pValueFilter 3.0:15.0
pValueFilterLimits 0.0:15.0
pValueFilterByRange on
The non-standard bed field pValue
, which
is floating-point, will be filtered by range. The expected data
range is 0.0 to 15.0, and by default only items with pValues within the 3.0 to 15.0
range will be displayed.
scoreFilter <low>[:<high>]
scoreFilterLimits <low>[:<high>]
Type bigBed
tracks can be filtered on the standard bed field
score
. This numerical filter is requested by the
scoreFilter
setting, which should include the default value.
By default the range
of values for a score filter is from 0 to 1000. However, you
can explicitly set the upper and lower limit of the filter by
setting scoreFilterLimits
.
The score filter will exclude items that fall below the setting. That is, a
scoreFilter of 800 will exclude all items with a score below 800.
Example:
scoreFilter 300
scoreFilterLimits 200:1000
The standard bed
field of score
, which is an integer will be used to filter items
in the track. By default, items with scores below 300 will be
excluded. The filter cannot be set to less than 200 or more than 1000..
filterBy <field1:title=[+]opt1a...>
[field2:title=[+]opt2a...]
NOT FOR HUBS. Not yet supported by bigBeds
Another method of
filtering items relies upon discrete values. One or more fields
such as name
or score
may contain a limited number
of discrete values that can be filtered on. These discrete values will be
displayed in a dropdown list from which the user can choose one or
more options. While the maximum number of options in the list is
not limited, displaying too many options can be confusing for the user.
Setting complexities:
- Because filters for different fields are delimited by whitespace, any
whitespace in titles and labels should be replaced by the '
_
'
(underscore) character.
- Each field/option pair is joined by '
=
' (equal sign).
- The field portion
can have a title that is delimited from the field name by '
:
(colon)'.
- A single field
filter will have multiple options delimited by commas.
- If the options are
a 1-based index (1,2,3...) then the option list can be preceded
with a '
+
' (plus sign) and the options themselves are only labels.
- Otherwise, each
option will be a value and optional label delimited by '
|
' (vertical bar).
Note that if one option has a label then all options of that filter
must have a label.
- Finally,
options may have CSS style wrapped in {curly} brackets and
appended to the end.
Because of this
complexity, please remember to use the '\
' continuation line to
ensure the setting is readable:
filterBy {field1}[:{Title1}]=[+]\
option1a[|label1a[{style1a}]],\
option1b[|label1b[{style1b}]],... \
[{field2}[:{Title2}]=[+]\
option2a[|label2a[{style2a}]],,...]
It is probable
that this setting will be redefined at some point, given that it
is very complicated. However, this current format will
be supported until entirely replaced.
Secret tricks:
- Avoid the use of the delimiter chars
,|:={}
in titles and
labels. (These characters can be included via HTML codes.)
Spaces can be included by using the '_
' character.
- The option labels
can be in color or have other CSS style attributes. Append the style
enclosed in curly brackets and containing no spaces. For example:
Pull_Over{color:#AA0000;text-decoration:blink;}
.
If one option has CSS style, then all options of that
filter must include a style definition.
- The filterBy option is implemented in the code using an SQL
where
clause.
For instance, filtering on the name
field for "Fred" and
"Ethyl" would result in an SQL where clause of
"where name in ('Fred','Ethyl')
". In type genePred
tracks, this knowledge is used to define filters on fields in a separate table!
This is done by defining the field as {otherTableName}.{fieldName}
.
The best way to
understand this setting is with an example. This is an operational
example in the hg19 "Open Chrom Synth" track.
Example:
filterBy color:Validation_Level=\
0|Validated_(OC_1){color:#000000},\
255|Open_Chromatin_(OC_2-3){color:#0000FF},\
39168|DNase_low_(OC_2){color:#009900},\
10027008|FAIRE_low_(OC_3){color:#990000},\
16711935|ChIP-seq_(OC_4){color:#FF00FF} \
ocCode:OC_Code=+\
One:_Validated_(all),\
Two:_DNase_(all),\
Three:_FAIRE_(all),\
Four:_ChIP_(all)
This setting sets up
two filters, one on the field "color
" and a second for the
"ocCode
" field. The color filter is given the title "Validation
Level". The second option has a value of "255" and a label
of "Open Chromatin (OC 2-3)". Note that it will appear
as blue in the list due to the {color:#0000FF} style definition.
Also notice that all options for this color field have a style
defined, even though the first option is black and would be so by
default. In this example, the only
whitespace within the setting value section immediately precedes the second filter
definition. The second filter, "ocCode
", is titled by the
inscrutable "OC Code". It is a numeric index filter
(as declared by the '+
'). The value of the second option is 2 and
only the label gets defined as "Two: Dnase (all)". Note
that the colon in the label is an HTML code.
The filterBy setting is very powerful. We recommend that you experiment with the
settings to determine which work best for your case.
itemRgb on
In bed formats supporting
at least 9 standard bed fields, this setting can be used to activate
item coloring using the value in the ninth field, itemRgb
. The
value of the item field must be an R,G,B triplet. When loaded
into a table, this field appears as an integer with the RGB values
in specific bits of the integer.
Example:
itemRgb on
maxItems <integer>
Maximum number of items to display individually in full mode. When the maximum is
exceeded, the excess items are drawn on top of one another on the last line.
In packed mode this refers to the number of lines rather than number of items.
Default: 250. For type bigBed
tracks, this setting can never
be larger than than 100,000.
Example:
maxItems 25
maxWindowToDraw <integer>
When too many individual bed items are shown in the Browser image (such as
might occur when a large region of a chromosome is viewed), the
information is often better visualized as a summary in dense mode.
Depending on the current visibility of the
bed track and which other tracks are being shown concurrently, the
Browser may automatically reduce the display to pack or dense mode. This setting
allows you to force the data summarization at whatever display limit you consider
reasonable. Unlike the maxItems
setting, which controls the display of
vertical space, this setting dictates the number of bases to be displayed horizontally
in a window before the track is forced into dense mode. There is no default for this
setting, but the maxItems
setting will ultimately prevent too many items from
being displayed.
Example:
maxWindowToDraw 200000
Browser images that show more then 200,000 bases will result in the track being
displayed in dense mode.
minGrayLevel <1-9>
When a bed track contains the standard
field score
, and when that score is used
to present items in gray or color scale (see
spectrum),
this setting specifies the lightest shade to be used.
This prevents the lowest scores from being displayed in too light of a color to easily
view. Set the value in the range 1 - 9, lightest to darkest.
Example:
minGrayLevel 4
This sets the lowest scores to slightly
less than medium gray, while the highest scores appear black.
noScoreFilter on
By default, bed
tracks with 5 or more standard bed fields that contain either a '.
' or
a '+
' in the type setting will be filterable on score
;
that is, they will have an assumed setting of "scoreFilter 0
". To turn
this old-style default off, include the "noScoreFilter
" setting.
Example:
type bigBed 6 +
noScoreFilter on
spectrum on
scoreMax <integer>
scoreMin <integer>
Replaces useScore
.
If your track is a
bed 5
or greater, then the standard bed score
field exists. This score, which is expected to vary from 0-1000,
can be used to control the shading of bed items drawn in the Browser
image. To activate this feature, set spectrum on
.
Lower scores will be shaded in light gray by default, while higher
scores will trend towards black. This can be modified in a number of ways:
-
color
can be used to replace gray scale with a color scale
-
altColor
with color
can vary items from
color to altColor
minGrayLevel
can be used to set the level of the lightest shade
-
scoreMin
and scoreMax
can be used to define the lower and upper limits of
the range that will receive graded shading
Example:
spectrum on
scoreMin 700
scoreMax 900
color 0,0,128
In this example, the track items will be
displayed in blue. Items with scores less than or equal to 700 will be shown in very
light blue,
those with scores between 700 and 900 will display in increasingly darker shades of blue,
and items
with scores greater than or equal to 900 above will display in dark blue.
searchIndex <str>
Specifies the list of field names on which a index has been made.
When a user enters a string in the position search box of the browser,
this index will be searched to find that name, and if the string is in
the index, the user will either be navigated to that position in the
browser, or if there are more than one matches of that string,
will be give a list of the positions to choose from. See HERE
for instructions on how to build an index for a bigBed file.
Example:
searchIndex name
searchTrix <url/relativePath>
Specifies the URL to a TRIX file that maps free text to
a set of indices that are assumed to have indicies in the associated
bigBed file. See HERE for instructions on how to build a TRIX file.
Example:
searchTrix url or relative path
thickDrawItem <off/on>
In bed tracks that
have 8 or more standard bed fields, portions of items in tracks such as
gene models can be drawn thicker to differentiate exon regions from introns.
When data is displayed at different scales, the items and the thick
portions of the items should scale proportionally. However, it
may be more important to see the existence of the thick regions
than it is to attempt to maintain the proportion. By setting
thickDrawItem on, the thick display regions of items are always drawn at a minimum
of 3 pixels, even when zoomed out greatly.
Example:
thickDrawItem on
bedFilter on
FOR BEDS ONLY
Activating this setting provides the bed filter type controls that allow you to filter
bed items by name with wildcard matching.
Example:
bedFilter on
The bed track will be be filterable by the bed
item names.
bedNameLabel <label>
When a user clicks on a bed track item in the Browser image,
the item detail page is shown. This setting specifies an
alternate label for the item name on that page. Without this
setting, the label will be "Item:".
Example:
bedNameLabel Gene Id
linkIdInName on
This setting changes the meaning of the bed name field
to "identifier description". If it is activated, the browser
does not show the first word of the BED item name,
but uses this first word for linking out to the item detail page. This
allows putting both an identifier, like a gene ID, and its human-readable
description into the BED item name field, separated by a space.
Example:
linkIdInName on
A BED name field of "9005 PITX2" will be shown "PITX2" on the genome
browser, but when the user clicks on it, the URL will be built only from
the first word, by default cgi-bin/hgc?i=9005&(...). The URL can be
changed with directUrl, where %s
is replaced by the identifier.
bigBed files are often created using the UCSC bedToBigBed program.
By default, this program expects only a single word for BED item names. To
tell the program to accept multiple words separated by spaces (required for
this track setting), you will need to use the -tab option for
bedToBigBed. This tells the program that that tab characters are
used instead of spaces to separate fields of the BED file. Please note that
this option will only work if tab characters are used as the field separator
throughout your BED file. More information on creating bigBed files is
available here.
Related settings:
baseColorUseSequence < <extFile {seqTable} <extFile> /
hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss >
NOT FOR HUBS. Not yet supported by bigBeds
Specifies where
item sequence can be found (if any) so that item sequence, or
differences from genomic sequence, can be drawn when viewing a
sufficiently small region.
- If
extFile
is
specified, two additional parameters are required, the name of
the seq table followed by the name of the extFile table to use
in looking up the sequence. These tables are loaded by hgLoadSeq.
- If
hgPcrResult
is specified than a PCR result is
used.
- If
lfExtra
is specified then the sequence of an item is found in the last
column of the table or remote file.
- If
nameIsSequence
is specified then the 4th column (name
or
sequence
) contains the sequence. (see
hg/lib/encode/tagAlign.as)
- If
seq1Seq2
is specified then the 7th & 8th columns (seq1
and seq2
)
contain the left and right pairs of the sequence. (see
hg/lib/encode/pairedTagAlign.as)
- If
ss
is specified then a
user provided a user provided blat sequence fole is looked for.
baseColorUseCds <given/table <table>>
NOT FOR HUBS. Not yet supported by bigBeds
Specifies where coding sequence (CDS)
coordinates can be found (if any) so that codons can be drawn
when viewing a sufficiently small region. If table
is
specified, an additional parameter of a table name, in cdsSpec
format, is required.
baseColorDefault
<diffBases/diffCodons/itemBases/itemCodons/genomicCodons>
NOT FOR HUBS. Not yet supported by bigBeds
Specifies the default drawing mode.
The itemBases
, itemCodons
, diffBases
and
diffCodons
options are applicable only if the track has sequence, as
specified by the baseColorUseSequence
setting.
The genomicCodons
, itemCodons
and diffCodons
are
applicable only if the track has CDS info, as specified by the baseColorUseCds
setting.
baseColorTickColor <lighterShade/contrastingColor>
NOT FOR HUBS. Not yet supported by bigBeds
Choose a contrastingColor
(this is often
white) or lighterShade
of color. This should be the
same color as would be chosen for the base text if the user were
zoomed in to base level.
showDiffBasesAllScales on
NOT FOR HUBS. Not yet supported by bigBeds
Show base differences for all zoom levels.
showDiffBasesMaxZoom <basesPerPixel>
NOT FOR HUBS. Not yet supported by bigBeds
Show annotations highlighting base or codon differences
only if current zoom level does not exceed
basesPerPixel
(a float). showDiffBasesAllScales
should also be set to make this useful.
showCdsAllScales on
NOT FOR HUBS. Not yet supported by bigBeds
Show CDS for PSL tracks at all zoom levels.
showCdsMaxZoom <basesPerPixel>
NOT FOR HUBS. Not yet supported by bigBeds
Use this setting (a float) to specify the maximum zoom-out allowed for displaying the CDS
for psl tracks.
In conjunction with this setting, showCdsAllScales
must be set on and
showDiffBasesMaxZoom
should be set to a value not more than showCdsMaxZoom
to make this
display configuration useful.
Examples:
baseColorDefault genomicCodons
baseColorUseCds given
showDiffBasesMaxZoom 10000.0
showCdsMaxZoom 10000.0
baseColorUseCds table hgFixed.transMapGeneUcscGenes
baseColorUseSequence lfExtra
baseColorDefault diffCodons
baseColorTickColor lighterShade
showDiffBasesAllScales .
showCdsAllScales .
exonArrowsDense <off/on>
On tracks that show
exons or blocks within items, exon arrows allow the user to jump to
the next exon/block outside the image. Use this setting to
display exon arrows even when the track is in dense mode.
itemDetailsHtmlTable <table>
NOT FOR HUBS. Supplemental table must be in local database.
Use this setting to specify a table, indexed by item name, that
contains an optional HTML fragment to display on the details page for
this item. The expected columns in the table are "name" and "html".
Example:
itemDetailsHtmlTable pseudoGeneDetails
itemImagePath <path> <suffix>
itemBigImagePath <path> <suffix>
Items can be
associated with images and the images can be made visible with
these two settings. The itemImagepath
specifies a
URL path to a directory with image files named in the format
{name}.{suffix}
. The name is retrieved from the table or remote data
file. This image will be displayed on the item detaiIs page. If
itemBigImagePath
is also supplied, then a link to a
larger image will be provided. If the path provided is local to
the browser then the path should be relative.
Example:
itemImagePath images/myTrackImages png
itemBigImagePath http://bigImages.com/myTrackImages jpg
When the user clicks
on a item named fred, then the item details page will show
the image images/myTrackImages/fred.png
and will also
provide a link to a larger image at
http://bigImages.com/myTrackImages/fred.jpg
.
mafTrack <trackName>
NOT FOR HUBS
By specifying a multiple alignments track, the item details page
will illustrate the differences for that item across a number of species.
Example:
mafTrack multiz46way
nextExonText <str>
prevExonText <str>
For tracks that
offer multiple block items such as gene models, the next/previous
exon arrows are usually displayed by default in the Browser. The functionality of
these tiny arrows is described by mouse-over "tool tips"
that default to "Next Exon" and "Prev Exon".
If the blocks do not represent exons, you can adjust the tool tip text to the
appropriate information with these two settings.
Example:
nextExonText "Next Match"
prevExonText "Previous Match"
showTopScorers #
Use this setting to
show a list of some number of top-scoring items in a region of the genome, when
looking at an individual item in the item details page. The
region will cover the current browser window coordinates.
Currently this setting is not configurable.
Example:
showTopScorers 20
Examples of item base types
type bed 3
The simplest bed
format, with nothing more than a chromosome and the start and stop
coordinates for each bed item. There is nothing to configure.
type bed 6 +
colorByStrand 255,0,0 0,0,255
...
type bigBed 6 +
colorByStrand 255,0,0 0,0,255
...
The type setting for
a bed and a bigBed are nearly identical. Here, both type settings
specify a track with the first 6 standard bed fields defined
(up to strand
) and with additional fields defined
after those 6 (indicated by the '+
'). The
colorByStrand
setting configures the plus strand items
to be colored red, while the minus strand items are blue.
type bigBed 8 .
scoreFilter 700
scoreFilterLimits 100:1000
thickDrawItem on
spectrum on
scoreMin 700
scoreMax 900
color 0,0,128
minGrayLevel 4
...
A bigBed track with
the first 8 standard bed fields (through thickEnd
),
and no additional fields. The '.
' tells
the Browser that the user may configure this track. The score
filter is explicitly declared to default to 700, and the defined
range of 100 - 1000 suggests there are no values of interest below 100.
This example also colors the items blue and presents
a spectrum or gradation of darkness based upon the score range.
Items with a score or 700 or less are displayed as the lightest shade of
blue, and items with a score of 900 or more are the darkest blue. Finally,
the minGrayLevel
ensures that the lightest shade is visible
to the user. No doubt the value of '4' was chosen after experimentation
with the Browser display.
type broadPeak
pValueFilter 2.0
pValueFilterLimits 0.0:300.0
This track is a
essentially a bed 6+3 format dataset, but it has been defined with
special features for ENCODE. The pValueFilter applies to a field
named pValue which is one of the 3 additional fields after the
standard 6.
Examples of item base types
type bigBed 6 +
colorByStrand 255,0,0 0,0,255
...
The type setting for
a bed and a bigBed are nearly identical. Here, both type settings
would define a track with the first 6 standard bed fields defined
(up to strand
) and with additional fields defined
after those 6. Notice that plus strand items are colored red,
while minus strand items are blue.
type bigBed 8 .
scoreFilter 700
scoreFilterLimits 100:1000
thickDrawItem on
spectrum on
scoreMin 700
scoreMax 900
color 0,0,255
minGrayLevel 4
...
A bigBed track with
the first 8 standard bed fields (through thickEnd
),
and no additional fields. The '.
' is required to tell
the Browser that the user may configure this track. The score
filter is explicitly declared to default to 700, and an allowable
range for the score suggests there are no values below 100 worth
looking at. This example also sets the items to blue and presents
a spectrum or gradation of darkness based upon the score range.
Items with score 700 or less are the lightest, and items with
score 900 or more are the darkest blue. Finally the lightest
shade set to be not too light with the poorly named minGrayLevel
setting. No doubt 4 was chosen after experimentation to see how
it actually looks in the Browser.
bigWig: Signal graphing tracks
Another set of common track types are those that graph a density signal along
the genome. The graph can be a continuously varying density plot or
one that displays a density signal in only certain regions. For data hubs
the most common signal track type is bigWig
.
For detailed specifications of the bigWig
remote data
file format and how to prepare it for display in the Genome Browser please
see:
http://genome.ucsc.edu/goldenPath/help/bigWig.html.
type wig <low#> <high#>
type bigWig <#> <#>
MySQL tables of type
wig
and remote data files of type bigWig
must declare the expected signal range for
the data.
Examples can be found below.
type bigWig <#> <#>
The remote data files of type bigWig
must declare the expected signal range for
the data.
Examples can be found below.
type bedGraph <field>
minLimit <#>
maxLimit<#>
The bedGraph type
track has the same file format as a bed file, but is loaded into
the MySQL database in a form that can be graphed. By default the
value to be graphed is the fifth standard bed field,
score
; however, you can specify a different field to use.
Typically only the first 3 standard bed fields are included
(chrom
, start
, stop
) and the fourth field
contains the signal value. The bedGraph track offers
a couple of important improvements over the wig track. In wig
tracks, the value of the signal is truncated into a single byte,
which is effective for graphing but fails at data storage. Also
the wig type was originally designed for fixed-size windowing, though
variations were added. The bedGraph type allows for variable
windowing and defining values even down to the base level. To be
clear, bigWig tracks are as versatile as bedGraphs. It is
only the wig format that suffers from these limitations.
On the other hand the storage density of wig, particularly the fixed step
variant, is vastly denser than bedGraph. In cases where the data is solely
meant for display, the 256 levels supported by wig more than suffice. For
single-base or even 10-base level resolutions, bedGraph is generally not practical
genome-wide. Note also that wigs converted to bigWigs do not suffer the reduced
precision of wigs loaded directly into the database. A bigWig based on fixedStep
wigs is the best way to represent dense graphs over the genome.
Note that the lower and upper limits of the bedGraph signal are not declared in the type,
but rather are declared with 2 separate settings, minLimit
and
maxLimit
.
Examples can be found below.
alwaysZero <off/on>
When autoScale is set to "on" in the signal track,
additionally setting alwaysZero
to "on" will ensure that the y=0
value will be in view at all times. Default: off.
autoScale <off/on>
The graph of the
data displayed in the Browser image is usually scaled on the y
axis in absolute coordinates. However, you can display the data
in autoScale which will ensure that the high score in the current
viewing window will peak at the top of the graph. Like most graph settings,
this is configurable by the user. Setting it to "on
" in trackDb will default
the track to autoScale
. Default: off.
NOTE: this option
should be avoided if it will lead to display regions in which a low signal
erroneously appears as significant because there is no high signal in the
view window.
Example:
autoScale on
graphTypeDefault points
The signal can be
graphed as either "points
" displayed at the signal
value, or the default space-filling "bar
".
Example:
graphTypeDefault points
maxHeightPixels <max:default:min>
The amount of
vertical viewing space for your signal track should be declared,
though it is configurable by the user. Typically it is set to no
more than 100 pixels and no less than 8, with a default of 16 or
32 pixels.
Example:
maxHeightPixels 100:16:8
The browser will display the track as 16 pixels high, but the user
can scale it up to 100 pixels.
maxWindowToQuery <integer>
For bigWigs only
When signal data is clicked in the Browser image, the details of the signal
in the current viewing window are displayed. For bigWigs that
reference remote data, the query can be a very expensive operation if the current window
is large. To avoid overburdening the Browser, the size of the window to
query should be limited. The value of this setting is the maximum window size in bases that
should be queried to give the detailed signal numbers.
negateValues <on>
Negate the values in the wiggle, meaning that positive values become negative and vice-versa.
This is useful for wiggles representing transcription or other activities on the Crick strand. Be aware that wiggles with negative values are drawn in altColor not color as positive values are.
spanList <s1>[,s2…]
NOT FOR HUBS. For wig tracks only.
Sets the data point span to just be the first span in table or list of spans in
the loaded table you can find the spans by doing:
"select span from <table> group by span
".
Typically spanList is only one as the example shows. Rarely there may be
more:
"spanList 1,1000
".
Special efforts must be made to load extra
spans into the table for special purposes.
Example:
spanList 1
smoothingWindow <off/1-16>
Often signal
information is chunky, because a single value is given for a number of
bases. The graph can smooth the chunky data, presenting a display
more reflective of the actual biology it is meant to illustrate.
The numerical value of this setting determines how much
surrounding data to use for smoothing: the larger the number, the
less abrupt the curves will be. The setting is user-configurable. Default: off.
Example:
smoothingWindow 4
transformFunc <NONE/LOG>
The track's signal
can be presented in log scale with this user-configurable setting. Default: NONE.
Example:
transformFunc LOG
viewLimits <lower:upper>
viewLimitsMax <lower:upper>
The data of most interest in a graph
track may be contained within a narrow range. Typically
high outlier values can skew a graph and very low values may
represent uninteresting data. Use viewLimits to set the default
viewing range. Also use viewLimitsMax as suggested outer bounds.
Example:
viewLimits 5:20
viewLimitsMax0:100
Any data points of 20 or above will be
shown as the peak of the graph. Data points that are below 5
will not be displayed. Even though the full data range extends to
100, these settings suggest that scores of 20 or more are all
considered highly relevant.
wigColorBy <bedTable>
NOT FOR HUBS. For wig tracks only.
Regions of the
graphed signal may be highlighted by color. Use a bed
table and the color
settings to shade regions of the wig
track.
Example:
wigColorBy myBed
color 175,150,128
altColor 255,128,0
The bed-type table "myBed" is used to highlight
regions of graphed signal based upon the scores in that table.
The table may itself be a visible track, or may exist only for the
purpose of highlighting the signal track.
windowingFunction <mean/mean+whiskers/maximum/minimum>
Depending upon how large of a genomic region
is displayed in the Browser image, it may be necessary to summarize
the actual signal. This user-configurable setting controls how the Browser
collapses the signal from (for example) 100 or 100 thousand bases down to
a single pixel. By default
the single pixel represents the mean
of the data, though the
maximum
or minimum
can alternatively be displayed. A more informative
option is often mean+whiskers
. This setting displays the
mean, max and one standard deviation above mean, differentiated by shading.
The mean is displayed as the darkest shade, one stdDev above mean as
slightly lighter, and the max as the lightest shade.
This subtle shading can quickly indicate if the
condensed data is hiding important information that can
be adequately evaluated only by zooming in.
Example:
windowingFunction mean+whiskers
When zoomed out, this track will show the mean
signal but include shading representing higher scores. The user
may change this setting.
yLineMark <#>
yLineOnOff <off/on>
gridDefault on
It can be useful to
draw a line across the track's signal graph at some fixed y
coordinate. Do this by setting yLineOnOff
to "on" and specifying the
y coordinate with yLineMark
. These two settings are
configurable by the user. Defaults: off and 0.0.
Often confused with
these configurable settings is the gridDefault
, which simply draws a
a line at y=0 across your entire track. This setting might be
useful if the lack of data is equivalent to a 0 signal.
Example:
yLineOnOff on
yLineMark 2.5
gridDefault on
The signal is graphed with a default solid line
at zero, suggesting that any gaps in data should be interpreted as
zero signal. There will also be a line at the signal height of 2.5
that may be used to emphasize which peaks in the signal reach
this critical height.
Examples of signal graphing tracks
type wig 0 100
windowingFunction maximum
viewLimits 5:20
viewLimitsMax 0:100
maxHeightPixels 100:16:8
spanList 1
wigColorBy myBed
...
This wiggle track is
composed of a MySQL table and binary "wib" files that
are referenced in the table. The default windowing
function is the maximum signal in each window (under each pixel)
shown. The span of bases covered by each row in
the table is identical and can be gathered from the first row in
the table. The wiggle has colors supplied by the bed
table, myBed.
type bigWig -0.25 37.6
windowingFunction mean+whiskers
viewLimits 5:20
viewLimitsMax 0:37.6
maxHeightPixels 100:32:8
yLineOnOff on
yLineMark 15
gridDefault on
color 128,0,128
...
This bigWig format
signal is held in a data file (which may be remote). The more
informative mean+whiskers windowing function is used by default in
this track, and the signal will be 32 pixels high in the Browser
image display. Note that even though the signal value may be
less than zero, that portion of the signal will not be
displayed. The Browser will display a line at y=0 and another at y=15, which
may be a threshold value for this signal. The track will be colored purple.
bedGraph 4
minLimit 0
maxLimt 20
viewLimits 5:8
viewLimitsMax 0:20
maxHeightPixels 100:16:8
...
This bedGraph style signal track is composed of
a MySQL table of items, each with a score defined in the fourth
column. While a wiggle track is usually composed of fixed
interval windows of signal (e.g. 200 bp), the bedGraph table may
define a signal in varying granularities of windows with or
without gaps.
Example of signal graphing tracks
type bigWig -0.25 37.6
windowingFunction mean+whiskers
viewLimits 5:20
viewLimitsMax 0:37.6
maxHeightPixels 100:32:8
yLineOnOff on
yLineMark 15
gridDefault on
color 128,0,128
...
This bigWig format
signal is held in a data file (which may be remote). The more
informative mean+whiskers windowing function is used by default in
this track, and the signal will be 32 pixels high in the Browser
image display. Notice that even though the signal value may be
less than zero, that portion of the signal will not be
displayed. The Browser will display a line at y=0 and another at y=15, which
may be a threshold value for this signal. The track will be colored purple.
type genePred [pepTable [mrnaTable]]
This type of track, based on MySQL tables, is for gene models and predictions.
- pepTable - Optional protein sequence table
- mrnaTable - Optional representative mRNA table
Note that missing
options can be filled with a '.
' dot. Additional settings
described below allow the grouping of gene models into classes and
the coloring and filtering of the models by class.
Examples can be found below.
Related settings:
geneClasses <cl1 cl2...>
Genes can be grouped into classes for the
purposes of coloring and filtering. The trick is how to
associate each named gene with its class. Use geneClasses
to create a
list of all gene class names delimited by white space.
gClass_<xxx> <red,green,blue>
Declare an RGB color for a named class.
itemClassTbl <table>
Declare a MySQL table that will link classes
to named gene models.
itemClassNameColumn <col>
Optionally declare the column of the
itemClassTbl that will hold the genePred names. Default:
name
.
itemClassClassColumn <col>
Optionally declare the column of the
itemClassTbl that will hold the class. Default: class
.
Example:
geneClasses rRNA tRNA snRNA
gClass_rRNA 255,0,0
gClass_tRNA 0,255,0
gClass_snRNA 0,0,255
itemClassTbl rnaTypes
itemClassNameColumn rnaName
itemClassClassColumn rnaType
In this genePred type track, RNA gene models
are divided into 3 classes that are colored red, green or blue.
The association of named gene models in the genePred table
with the three classes is defined in the "rnaType" table.
That table holds the RNA type in the "rnaType" column and the
gene name in the "rnaName" column.
filterBy <field1:title=[+]option1a...>
[field2:title=[+]opt2a...]
Filtering gene models by table column or even
itemClassTbl column can be achieved by this setting. Complete
description of this setting can be found in the
bed/bigBed item-based track settings. Here is an example for
referencing the class as found in the table defined by itemClassTbl
. Not all
track types will support externally referenced tables using filterBy
as genePred
type does. But if you understand the CGI code that
performs the table select, then filterBy can provide a powerful extension to
the SQL selection used.
Example:
geneClasses rRNA tRNA snRNA
gClass_rRNA 255,0,0
gClass_tRNA 0,255,0
gClass_snRNA 0,0,255
itemClassTbl rnaTypes
itemClassClassColumn rnaType
filterBy rnaTypes.rnaType:Class=\
rRNA|Ribosomal_RNA{color:#FF0000},\
tRNA|Transfer_RNA{color:#00FF00},\
snRNA|Small_Nuclear_RNA{color:#0000FF}
When gene models are
selected from the genePred table for display in the Browser,
their class is also selected from the "rnaTypes" table. Using the
filterBy
setting creates a user selectable drop-down list box of
3 choices or "all". When the user filters by tRNA and snRNA (the
green and blue choices), the mySQL select statement used by the
Browser will be limited by the where clause "where
rnaTypes.rnaType in ('tRNA','snRNA')
".
autoTranslate 0
By default, a
predicted protein translation is generated for a gene model when
a user views it on the details page. This feature may be blocked
by setting autoTranslate
to zero.
Example:
autoTranslate 0
The genPred track
will NOT show auto-generated protein sequence, perhaps because
this track is for RNA genes.
intronGap <#bases>
In drawing gene models, it can be useful to see
"exon arrows" when the transcript extends beyond the current
window. This setting, which defaults to zero, ensures that these
arrows will not be drawn if the interceding intron gap is less
than the stated number of bases.
Example:
intronGap 12
Don't draw exon arrows when the gap between
exons is 12 bases or less.
defaultLinkedTables <table1>[,table2...]
In hgTables, when selecting output fields,
display these all.joiner-linked tables by default.
Example:
defaultLinkedTables kgXref
idXref <idColumn> <altIdColumn>
By using this setting you can link alternative
names to the gene models found in a genePred. This is used by
the Table Browser to establish links to other tables.
Example:
track knownGenes
idXref kgAlias kgID alias
The ID in the name column of the knownGenes
table is related to the alias found in the kgAlias table.
oldToNew <tableName>
In successive versions of gene models, it can
be helpful to map older genes to their newer models. This can be
done by providing a MySQL table that maps the change, and then using
this setting to ensure the gene details page shows any changes.
Example:
track knownGeneOld5
oldToNew kg5ToKg6
The older version of UCSC Genes references
changes that are seen in the newer version.
Examples of genePred tracks
type genePred
oldToNew kg5ToKg6
baseColorUseCds given
baseColorDefault genomicCodons
geneClasses coding nonCoding pseudo
itemClassTbl myClasses
gClass_coding 12,12,120
gClass_nonCoding 0,153,0
gClass_pseudo 255,51,255
filterBy myClasses.transcriptClass:Class=\
coding{color:#0C0C78},\
nonCoding{color:#009900},\
pseudo{color:#FF33FF}
...
Gene model track
with defined classes and the option to filter by the color-coded
classes. Note the base level coloring option.
type genePred . mrna
url http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=hg17&l=$$
urlLabel AceView Gene Summary:
This gene prediction
track has associated representative mRNAs found in the "mrna"
table. There is also an "AceView Gene Summary" url
presented on the details page.
type bam
Declares configuration settings for a track of type bam. If the bigDataUrl
setting is included, that data at the location specified by that URL will be
displayed. Otherwise, a database table with a single column fileName
can specify the location of a local file or a URL.
If the database table includes a column seqName
, a different
BAM file or URL can be specified for each assembly sequence.
Example can be found below.
Related settings:
bamColorMode <strand/gray/tag/off>
There are numerous ways to color bam tracks
to highlight certain aspects of the data. All of these are
user-configurable.
Possible settings:
strand
: (Default) When colored by strand, mismatched bases are highlighted in
bright red, alignments on the reverse strand are
colored dark red, and alignments on the forward strand are
colored dark blue.
gray
: When colored in grayscale, items are shaded according to the
method specified by bamGrayMode
: alignment quality, base qualities, or unpaired
ends.
tag
: Colors are specified in "user-defined tags". SAM/BAM may
include user-defined tags, the names of which begin with X, Y or Z and include one other letter
or number. The user-defined tag named here specifies red, green and blue (RGB) intensities
as a zero-terminated string (tag type Z) containing comma-separated triples of numbers
from 0-255. For example, if a SAM/BAM record includes the tag YC:Z:255,0,0, then the
item is colored red; YC:Z:0,0,255 makes the item blue. By default, the tag is "YC" unless
changed using the bamColorTag
setting.
off
: No additional coloring.
bamGrayMode <aliQual/baseQual/unpaired>
aliQualRange <min:max>
baseQualRange <min:max>
When bamColorMode
is set to "gray", you
can highlight one of the following:
aliQual
: (Default) The "alignment qualities" of the items are
shaded on a scale of 0 (lightest) to 99 (darkest). Use aliQualRange
to specify a default range.
baseQual
: "Base qualities" are shaded on a
scale of 0 (lightest) to 40 (darkest). Use baseQualRange
to specify a default range.
unpaired
: When "unpaired ends" is selected, an item that
was paired in sequencing but whose mate was not mapped is colored gray,
while singletons and properly paired items are colored black.
Refer to the
SAM format details
for a discussion of these values.
bamColorTag <XX>
You can also use RGB data associated with
individual tags within the bam file itself. Refer to the
SAM documentation
to understand how the RGB values are included.
When the bamColorMode
is set to "tag", the standard "YC" tag
is used as the default. The default may be overridden with this setting.
noColorTag .
The bam coloring options are all user-configurable within the browser. If your
bam dataset contains no color tags, this setting should be included to block the
Browser from offering the option to color tags by an embedded RGB value.
Examples:
bamColorMode strand
noColorTag
Sets the bam to use the default coloring scheme based on strand alignment. At the same time,
the bam track will not offer the option to color the tags by
RGB values, perhaps because this bam has no RGB values.
bamColorMode gray
bamGrayMode aliQual
aliQualRange 20:80
These settings
will highlight tags by alignment quality score. If the score
is at 80 or above, the tag is shaded black; if it is less than
20, the tag is shaded very light gray.
bamColorMode tag
bamColorTag YC
The bam file includes RGB values in the YC
field that will be used to color tags.
bamColorMode off
No special coloring will be applied to items.
bamSkipPrintQualScore .
Any bam tag can be
displayed on the details page by clicking on it in the Browser
image. The details include quality scores by default. If these
scores are not relevant for this particular bam, they may be excluded
from the details page with this setting.
Example:
bamSkipPrintQualScore .
indelDoubleInsert <off/on>
indelQueryInsert <off/on>
indelPolyA <off/on>
Insertion and deletion
differences between tag sequences and the reference genome can be
highlighted with the use of these settings. These options may be
set by the user.
-
indelDoubleInsert
: Use to highlight alignment gaps in both the target
(reference) and query (tag) sequence with double (=) lines.
-
indelQueryInsert
: Use to highlight an insert in the query
sequence only by drawing an orange (|)
or purple (|) vertical line.
Orange lines show unalignable regions in the middle of a sequence,
and purple highlights regions at the end of the query sequence.
indelPolyA
: Use to highlight an apparently valid
poly-a tail by drawing a vertical green line (|).
Example:
baseColorUseSequence genbank
indelDoubleInsert on
indelQueryInsert on
indelPolyA on
minAliQual <#>
When the Browser image is zoomed in to the level where individual tags are visible, the
tags in a bam file can be filtered to show only those with a minimum alignment quality score.
This is a user-configurable setting. Default: 0.
Example:
minAliQual 20
Related settings:
pairEndsByName .
Some high-throughput sequencing technologies
result in "paired end" tags, which are two individual bam
records joined by their name. If this is the case with your
dataset, include this setting.
pairSearchRange <#>
Searching to join pairs of tags by name
will be limited to a maximum distance (default: 20,000
bases). Use a larger range to increase the likelihood that both
reads in a pair will be found even when only one read is in
the viewed region. Use a smaller range to speed image rendering.
Example:
pairedEndsByName .
pairSearchRange 5000
The dataset includes paired end tags. The maximum search range to join tag pairs
by name is capped at 5000.
showNames <on/off>
When the Browser image is zoomed in to the level where individual tags are viewable,
the query name for each tag is shown by default. Use this setting to hide this name.
Example:
showNames off
Example of a bam track
type bam
bigDataUrl http://hgdownload/ucsc.edu/goldenPath/hg19/bambam/barneysSon.bam
pairEndsByName on
showNames off
bamColorMode off
bamGrayMode aliQual
indelDoubleInsert on
indelQueryInsert on
maxWindowToDraw 10000
...
The bam data is held in the file "barneysSon.bam" which is at an
internet-accessible location. In addition to the data file, an
associated index file must reside at the same location. The index file must have the
same name as the data file, with ".bai" appended (e.g. barneysSon.bam.bai
).
type psl <subtype> [otherDb]
The psl type tracks
require the specification of a subtype: est
, mrna
,
protein
or xeno
. The default, which is
represented as ".", is regular human mRNA. When the xeno
subtype
is selected, an additional optional parameter may be set to specify the other species
assembly. If present, the alignments can be color-coded by
chromosome, and the chromosome and position (in kilobases) are shown
in the alignments label.
Examples can be found below.
blastRef <assembly.table>
Include a blastRef
to an assembly and table that contains geneId and position
retrievable by accession id. This information will be displayed
in the item name.
Example:
blastRef hg17.blastKGRef02
colorChromDefault off
For psl tracks of
subtype xeno
, the alignments may be colored to indicated their
location in the other species. This setting is turned on by default
when the other species is specified in the type psl
setting. Use this setting to turn off chromosome coloring by default,
offering the user the choice to turn it on.
Example:
type psl xeno loxAfr1
otherDb loxAfr1
colorChromDefault off
pred <assembly.table>
Use the pred setting
to name an assembly and table containing protein sequence data for
the named alignments.
Example:
pred hg18.blastKGPep04
pslSequence <no/all/different>
This setting specifies some display configuration options for
psl tracks that also have sequence loaded.
all
: Display nucleotide labels on all bases.
different
: Label only base differences.
no
: Allow the user to select which of the other two options is preferred.
Example:
pslSequence different
transMapGene <assembly.table>
transMapInfo <table>
transMapSrc <assembly.table>
transMapTypeDesc <label>
For alignment tracks generated using the TransMap cross-species alignment
algorithm, these settings are used to connect the transMap
detailed information with the alignments.
transMapInfo
: Use to name the table in the current assembly that
ties an alignment with the source assembly and feature.
transMapSrc
: Use
to name the table in the source species assembly that contains
the details of the feature's source location.
transMapGene
: Use to name the table mapping the alignment
to gene names in the relevant species. Note that tables that are
common to multiple species should be put in the hgFixed
database.
transMapTypeDesc
: Use to
set a label for the type of transMapping that the alignment covers.
Example:
transMapInfo transMapInfoUcscGenes
transMapSrc hgFixed.transMapSrcUcscGenes
transMapGene hgFixed.transMapGeneUcscGenes
transMapTypeDesc UCSC Gene
baseColorUseCds table hgFixed.transMapGeneUcscGenes
baseColorUseSequence extFile hgFixed.transMapSeqUcscGenes
Note that several of the named tables are in
hgFixed
, which is a database containing tables that
are shared by multiple species and assemblies. Also notice that
the same table that was named in transMapGene
is
also used in this example for baseColorUseCds
.
ucscRetroInfo
For alignments
illustrating retrotransposition, use this setting to name a table
with details of the source location.
Example:
ucscRetroInfo ucscRetroInfo1
Examples of psl alignment tracks
track ucscRetroAli1
type psl
ucscRetroInfo ucscRetroInfo1
baseColorDefault diffCodons
baseColorUseCds table ucscRetroCds
baseColorUseSequence extFile ucscRetroSeq1 ucscRetroExtFile1
indelDoubleInsert on
indelQueryInsert on
showDiffBasesAllScales .
showDiffBasesMaxZoom 10000.0
...
In this example of
retroposed genes, mature mRNA has been aligned to the genome.
Notice there is a ucscRetroInfo table that describes the
non-transposed gene location. Also notice the use of the
baseColor settings for coloring the coding sequence (CDS).
track protBlat
color 0,100,0
altColor 255,240,200
type psl protein
...
In this example of
protein sequence blat results, the color of matching sequence is
green, while indels (in this case introns) are highlighted with
yellow.
track rgdEst
spectrum on
color 12,12,120
type psl est
...
This expressed
sequence tag example will have colored alignments that are graded
by a score thanks to "spectrum on
". Though psl tracks do not have
a score
column as part of the format, a score is
generated based upon matches and mismatches in the alignment. The
shading is even more subtle in that the weight given to inserts
varies depending upon whether the alignment is to the same or a
different species.
track blastzTetNig1
color 0,0,0
altColor 50,128,50
spectrum on
type psl xeno tetNig1
otherDb tetNig1
...
This psl track is for foreign species or "xeno"
alignments, in this case the sequence reads of a species of fish
aligned to human.
type chain <otherDb>
otherDb <otherDb>
Tracks of type chain
show sequence alignments
from another species to the reference genome. This type
requires the assembly database of the other species to be named in both the
type setting and in the "otherDb
" setting.
Example can be found below.
type netAlign <otherDb> <otherChainTable>
otherDb <otherDb>
Tracks of type netAlign show the best chains of
sequence alignments from another species to the reference genome.
Gaps are filled in levels, where possible. This type requires the
assembly database of the other species to be named in both the type setting and
in the "otherDb
" setting.
Example can be found below.
chainColor <scheme>
By default chains are colored by the alignment
chromosome of the query species. This can be overridden with this
setting. The three options are:
Chromosome
- default
Normalized Score
- chains are colored by score
Black
- no coloring occurs
This setting affects
chain
but not netAlign
type tracks.
Example:
chainColor Black
chainLinearGap <loose/medium>
The chainLinearGap setting should reflect the
"-linearGap
" parameter used in axtChain to generate
the track. It represents the gap scoring matrix used and will be
either:
loose
- chicken/human linear gap costs
medium
- mouse/human linear gap costs
This setting is for both chain
and netAlign
type tracks.
Example:
chainLinearGap medium
chainMinScore <#>
The chainMinScore setting should reflect the
"-minScore
" parameter used in axtChain to generate the
track. It represents the score threshold for chains to be
included in the set. Default is 1000. This setting is for both
chain and netAlign type tracks.
Example:
chainMinScore 5000
chainNormScoreAvailable <yes/no>
A given chain or netAlign track may or may not
have a populated normScore column. If the column exists, then
its value can be displayed in the item details page of the
Browser by setting chainNormScoreAvailable to yes
.
Item coloring based upon score as selected by the
chainColor Normalized Score
setting also requires
this setting to be yes
.
Example:
chainNormScoreAvailable yes
chainColor Normalized Score
matrix <size> <#,#,#,#,…>
matrixHeader <b1,b2,b3,b4>
$matrix
token in html.
The method for scoring and selecting chains and
generating netAligns relies upon a matrix of costs for base
substitutions. The matrix used in the generation of any given
paired alignment can vary depending upon such things as
evolutionary distance and the species involved. The matrix used
can be dynamically included in the HTML description using three
elements:
- The HTML description must have the
$matrix
token in it.
- The
matrix
to be used must be defined
with this trackDb setting. The format of this setting is the cell
size of the matrix which for DNA alignments is 16. This size is
separated by a space from the comma-delimited array of all the
values as the matrix cells are filled in left to right and top to
bottom.
- The
matrixHeader
setting should be
used to define the order of base transitions in the matrix.
Typically it is “A,C,G,T “.
Example:
html chainNet
matrixHeader A,C,G,T
matrix 16 91,-114,-31,-123,\
-114,100,-125,-31,\
-31,-125,100,-114,\
-123,-31,-114,91
Here the $matrix
token found in the
chainNet.html file will be replaced by the following matrix:
A C G T
A 91 -114 -31 -123
C -114 100 -125 -31
T -31 -125 100 -114
G -123 -31 -114 91
Examples of chain and netAlign tracks
track chainRheMac2
type chain rheMac2
otherDb rheMac2
color 0,0,0
altColor 100,50,0
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A,C,G,T
chainMinScore 3000
chainLinearGap medium
html chainNet
...
track netRheMac1
type netAlign rheMac1 chainRheMac2
otherDb rheMac2
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A,C,G,T
chainMinScore 3000
chainLinearGap medium
html chainNet
...
Both the chain and netAlign tracks above are
for alignments of the query species/assembly rheMac2
against the target species determined by the database this trackDb
belongs to (e.g., human/hg19). Because the netAlign track is
based upon the data in the chain track, it references the track in its
type setting. Both tracks use the same matrix, chainMinScore and
linear gap settings. Methods to group these two tracks into a
single set that share settings are described later in this
document.
type wigMaf <minVal> <maxVal>
A wigMaf type track
is composed both of MAF format alignment (loaded with hgLoadMaf).
The track may optionally include one or more conservation signals. The
signals must be within the same data range defined with the min
and max values in the type setting.
Examples can be found below.
frames <table>
A wigMaf track can
display gene codon translation. The reading frame may differ
between species. By providing the reading frames information in a
separate table, the user can choose which frame to use when
viewing the data.
Example:
frames myCodonFrames
irows off
By default, gaps in the non-reference species are filled with the placeholder
character:
- Single Line '
-
': No bases in the aligned species. Possibly
due to a lineage-specific insertion between the aligned blocks in the human genome
or a lineage-specific deletion between the aligned blocks in the aligning species.
- Double line '
=
': Aligning species has one or more unalignable
bases in the gap region. Possibly due to excessive evolutionary distance between
species or independent indels in the region between the aligned blocks in both species.
- Pale yellow coloring:
Aligning species has Ns in the gap region.
Reflects uncertainty in the relationship between the DNA of both species, due
to lack of sequence in relevant portions of the aligning species.
These display conventions make it easier to visualize the columns in stacked
alignments, but they also tend to clutter the display. The user has the option to remove
these placeholders by unchecking the "Display chains between alignments" option. To
set the default of this option to off, set irows
to "off
".
Example:
irows off
itemFirstCharCase noChange
This controls if
species names in the multiple alignment should be capitalized in
the pairwise display. Set "noChange
" to avoid forcing
the first letter to lower case.
Example:
itemFirstCharCase noChange
pairwiseHeight <#>
A wigMaf display in
the Browser image is a stacked set of pairwise alignments to the
target genome. Using this setting, you can change the height of
each pairwise signal in the image.
Example:
pairwiseHeight 10
speciesCodonDefault <species>
This setting, which
is used with "frames", declares the default species
for the codon reading frame.
Example:
speciesCodonDefault hg19
frames myCodonFrames
speciesDefaultOff <species1> [species2 ...]
To control which of
the stacked pairwise alignments are displayed or hidden by default, use
speciesDefaultOff
to list the species alignments that will not be
displayed. Each species is specified as in the MAF
file Organism names except embedded dots and/or spaces
are replaced with underscores (e.g. C. elegans ->
c_elegans).
Example:
speciesDefaultOff galGal2 fr1 danRer1
Related settings:
speciesOrder <species1> [species2 …]
Use speciesOrder
to declare the order of the
stacked alignments. If there are many species in your track,
it may make sense to use the speciesGroups
setting instead.
speciesGroups <sgroup1> [sgroup2 …]
sGroup_<sgroupN> <species1> [species2 …]
You can include a list of "clades"
to group the species into. This option is an alternative to
speciesOrder
, used when there are many species. Each
speciesGroup
in the list must have its own setting
(sGroup_<group>), followed by a list of species,
specified as for speciesOrder.
Examples:
speciesOrder panTro1 canFam1 mm5 rn3 \
galGal2 fr1 danRer1
speciesGroups Mammal Vertebrate
sGroup_Mammal mm9 rn4
sGroup_Vertebrate galGal2 fr1 danRer1
Choose one of these two alternatives to display species.
speciesUseFile <fileName>
Deprecated
Much more rarely used, this setting can
replace speciesOrder
and speciesGroups
.
Set the speciesUseFile
to a path relative to the apache cgi-bin.
The file should contain a single species name as the first word of each line.
Example:
speciesUseFile speciesLists/conserved8Way.txt
summary <tableName>
This setting contains table name of MAF summary table. The summary
view is used when the browser display is zoomed out to contain a million
or more basepairs. A summary table is created from a multiple alignment MAF
file using the utility hgLoadMafSummary
.
Example:
summary hg17Maf8waySummary
treeImage <imageFile>
The phylogenetic tree
can used to show the relations of the species in the multiple
alignment should be included as an image file. This path is
relative to the htdocs images directory (usually /images).
Example:
treeImage phylo/hg17Maf8way.jpg
wiggle <table1> <leftLabel1> <uiLabel1>
[table2 leftLabel2 uiLabelN ...]
Optionally more than
one conservation signal can be included with your MAF display by
using this setting. When you include conservation wiggles, you
can also include the standard settings for controlling signal type
tracks. The setting includes three parts, then (optionally)
additional sets of three, all delimited by white space. The first
table is the default. The leftLabel
is used to
prefix the label "Cons" in the left label area of the Browser
image. The uiLabel
is displayed in the track
configuration page. If only one table is listed, and no label is
present, the default label "Conservation" will be
displayed. The labels cannot contain spaces, but underscores (_
)
will be translated to spaces in the display.
Note: directly
pairing the conservation signals within the wigMaf track is an
older way of doing things. It is easier to give users control of
what they want to see, by including your wigMaf track and separate
signal type tracks as subtracks within a composite track. See the
composite track description below.
Example:
wiggle phastCons8wayMammal Mammal Placental_Mammal \
phastCons8way Vertebrate Vertebrate
Examples of wigMaf tracks
track hg17Maf8way
type wigMaf 0.0 1.0
summary hg17Maf8waySummary
wiggle phastCons
treeImage phylo/hg17Maf8way.jpg
speciesOrder panTro1 canFam1 mm5 rn3 galGal2 fr1 danRer1
speciesDefaultOff galGal2 fr1 danRer1
irows off
pairwiseHeight 10
maxHeightPixels 100:16:8
viewLimits 0.5:0.9
viewLimitsMax 0.0:1.0
...
This 8-way
multi-alignment for the hg17 human assembly is defined to include
a summary table, tree image and one wiggle table containing the
conservation score for the 8 species. Notice that the pairwise alignments
for the last three species are turned off by default, and each
pairwise alignment will have a height of 10 pixels. With few
species displayed by default, irows defaults to "off" as
well, which will result in a cleaner display. Since there is a
conservation wiggle, there are additional settings for that
signal.
track multiz46way
type wigMaf 0.0 1.0
summary multiz46waySummary
frames multiz46wayFrames
speciesCodonDefault hg19
itemFirstCharCase noChange
treeImage phylo/hg19_46way.gif
speciesGroups Primate Placental_Mammal Vertebrate
sGroup_Primate panTro2 gorGor1 ponAbe2 rheMac2 papHam1 calJac1 tarSyr1 micMur1 otoGar1
sGroup_Placental_Mammal tupBel1 mm9 rn4 …
sGroup_Vertebrate macEug1 monDom5 ornAna1 …
speciesDefaultOff panTro2 gorGor1 ponAbe2 papHam1 …
pairwiseHeight 10
...
For this wigMaf
track, there is no wiggle defined. In this actual
example taken from the hg19 Genome Browser, the several conservation signals
displayed in concert with this multiple alignment are separate
signal-type tracks defined as part of the "Conservation"
composite track (see discussion of composites below). Notice
that the 46 species in this alignment are organized into clades
using the "speciesGroups
" setting. Each clade has its
own "sGroup
" setting to declare the order within (not
all species shown).
type expRatio
Microarray data is
displayed in the Browser by expRatio
type tracks.
The type requires additional settings: expScale, expStep and
groupings.
Example can be found below.
expDrawExons on
If microarray data
includes gene model or blocks within items, then the data can
be viewed as exons and introns by setting expDrawExons
to on. The setting is configurable by the user.
Example:
expDrawExons on
expScale <#>
Maximum expression
value.
Example:
expScale 3.0
expStep <#>
Amount to step in
visible expression scale. A round number close to expScale
divided
by 8 is best.
Example:
expScale 3.0
expStep 0.5
expTable <tableName>
This setting specifies
the name of a table in the common hgFixed
database that contains names of experiments, etc.
groupings <fileName>
A microarray dataset
must refer to a specific set of configurations to load from the
microArrayGroups.ra file. Please refer to the
microarray track
section of the UCSC genomewiki
for detailed instructions on the location of this file and its
format. Use the "groupings
" setting to point to a stanza keyed on
"name
" in that file.
Example:
groupings gnfHumanAtlas2Groups
Example of an expRatio track
track sestanBrainAtlas
type expRatio
expScale 3.0
expStep 0.5
expTable sestanBrainAtlasExps
groupings sestanBrainAtlasGroups
...
This microarray dataset refers to groupings
defined in the "gnfHumanAtlas2Groups
" stanza of the
makeDb/hgCgiData/Human/microarrayGroups.ra file.
type bed 6 + # Track name starts with "snp"
followed by the 3-digit dbSNP build number
UCSC's subset of dbSNP could be described as "bed 6 + 19"
and is produced by a complex process starting with downloading
several database dump files and fasta files from dbSNP, and ending
with the creation of snpNNN and several auxiliary data
tables. This type is not supported as a custom track type.
chimpDb <db>
If chimp chains/nets were used to identify the chimp reference
assembly allele at the location homologous to the human SNP, this
specifies which chimp genome assembly was used, e.g. panTro2
.
chimpMacaqueOrthoTable <table>
If chains/nets from chimp and rhesus macaque were use to identify
the chimp or macaque reference assembly allele at the location
homologous to the human SNP, this specifies the database table
that contains the mapped alleles.
chimpOrangMacOrthoTable <table>
If chains/nets from chimp, orangutan and rhesus macaque were use to identify
the chimp/orangutan/macaque reference assembly allele at the location
homologous to the human SNP, this specifies the database table
that contains the mapped alleles.
codingAnnoLabel_<table> <text>
Deprecated; will probably be removed.
This specifies a text label for display of <table>'s
predictions of a SNP's effect on a protein-coding gene.
codingAnnotations <table>[,table]
Deprecated; will probably be removed.
This specifies one or more tables containing predictions of SNP
effects on protein-coding genes.
defaultGeneTracks <genesTrack>[,genesTrack]
The details page of a SNP can display the predicted functional
affect on a gene from any genePred track.
Since there are often many gene tracks and models, the prediction
will depend upon the gene model used. The user has a chance to
choose from those available, but this setting establishes
a default gene track or tracks to base predictions on.
Example:
defaultGeneTracks knownGenes
defaultMaxWeight <1|2|3>
dbSNP assigns a weight of 1, 2 or 3 to each variant, depending
on how many distinct mappings a variant's flanking sequences have
to the genome.
If this is set to 1
, only uniquely mapped variants will
be displayed by default. If 2
, only uniquely mapped
variants and variants with a small number of duplicate mappings will
be displayed. If 3
, all variants will be shown regardless
of weight. Note: some tables such as snpNNNCommon and
snpNNNFlagged contain only uniquely mapped variants, so this
setting has no effect on those tables.
hapmapPhase <II|III>
The SNP details page looks for the SNP's ID in HapMap track tables
that have different names and contents depending on whether they
were loaded from HapMap phase II or HapMap phase III data.
(This setting is also used by HapMap SNPs tracks.)
macaqueDb <db>
If macaque chains/nets were used to identify the macaque reference
assembly allele at the location homologous to the human SNP, this
specifies which macaque genome assembly was used, e.g. rheMac2
.
orangDb <db>
If orangutan chains/nets were used to identify the orangutan reference
assembly allele at the location homologous to the human SNP, this
specifies which orangutan genome assembly was used, e.g. ponAbe2
.
snpExceptions <table>
This specifies an auxiliary table that contains annotations of unusual
properties of variants. This setting applies only to versions prior to dbSNP
build 132; starting with build 132, exceptions are incorporated into the
main snpNNN table and an auxiliary table is no longer needed.
snpExceptionDesc <table>
This specifies an auxiliary table that maps exception keywords
to one-sentence descriptions.
snpSeq <table>
This specifies an auxiliary table that maps variant IDs to
file offsets at which flanking sequences are stored.
snpSeqFile <path>
This specifies an auxiliary file that contains the flanking
sequences of each variant's representative submitted SNP.
Example of a SNP track
track snp135Common
shortLabel Common SNPs(135)
longLabel Simple Nucleotide Polymorphisms (dbSNP 135) Found in >= 1% of Samples
group varRep
priority 99.0911
visibility dense
url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
urlLabel dbSNP:
snpSeq snp135Seq
snpExceptionDesc snp135ExceptionDesc
defaultGeneTracks knownGene
maxWindowToDraw 10000000
type bed 6 +
This track displays variants from dbSNP build 135 with Minor Allele Frequency (MAF)
of at least 1%. Flanking sequence file offsets come from the snp135Seq table,
descriptions of unusual properties are taken from the snp135ExceptionDesc table,
and effects of variants on protein-coding genes are shown with respect to the table
knownGene (UCSC Genes track) by default. If the viewed region is more than
10,000,000 base pairs, the data will not be loaded and drawn.
type vcfTabix
If the bigDataUrl
setting is included, the data at the location
specified by that URL will be
displayed. Otherwise, a database table with a single column fileName
can specify the location of a local file or a URL.
If the database table includes a column seqName
, a different
VCF file or URL can be specified for each assembly sequence.
Example can be found below.
hapClusterEnabled <true|false>
If the VCF file includes genotype columns for at least two individuals,
then a haplotype sorting display is enabled by default. This option can be
used to disable it if desired, for example if the genotypes have not been
phased and a significant portion of the genotypes are heterozygous.
More information about the haplotype sorting display can be found
here.
hapClusterColorBy <altOnly|refAlt|base>
Assuming hapClusterEnabled
is true
,
this specifies one of three ways that reference and alternate alleles are colored:
altOnly
: reference allele is white (invisible),
alternate allele is black. This emphasizes haplotypes with alternate alleles. (default)
refAlt
: reference allele is blue, alternate allele is red.
base
: A is red, C is blue, G is green and T is magenta.
hapClusterTreeAngle <triangle|rectangle>
Assuming hapClusterEnabled
is true
,
this controls the shape of leaf clusters on the right of the tree
(i.e. the lines drawn to denote groups of identical local haplotypes):
triangle
for the < shape (default), rectangle
for the [ shape.
hapClusterHeight <N>
Assuming hapClusterEnabled
is true
,
this specifies the height in pixels of the haplotype sorting display.
applyMinQual <true|false>
If true
, then variants whose QUAL column contains a value less
than the minQual
setting will not be displayed.
minQual <Q>
Assuming applyMinQual
is true
,
this is the minimum QUAL value required for a variant to be displayed.
minFreq <F>
The minimum minor allele frequency required for a variant to be displayed.
By default this is 0.0 (i.e. display all variants).
Example of a VCF track
track myVcf
type vcfTabix
bigDataUrl http://myorg.edu/mylab/myVcf.gz
hapClusterEnabled false
maxWindowToDraw 3000000
...
The data for this VCF track is stored in the remote file,
"myVcf.gz". That file is paired with a tabix-generated index file named
"myVcf.gz.tbi" found in the same remote location.
type pgSnp
Personal Genome SNP
type tracks are essentially in "bed 4 + 3" format.
The fourth column, name
, is filled with one or more variants
(including insertions and deletions) delimited with a '/
'
character. The fifth column contains the number of variants found
in the name
column, while the sixth and seventh columns contain
comma-delimited arrays of frequencies and scores respectively.
Files in this format can be loaded into MySQL with hgLoadBed using
the "pgSnp.sql" schema.
The browser image
displays variants as stacked boxes that show the frequency for
each variant, if that information is in the table. The details page for each variant item
computes any amino acid change if the variant is
in a coding region.
pgPolyphenPredTab <table>
Not supported for custom tracks
Auxiliary table with likelihoods of variant damage to proteins from polyPhen.
pgSiftPredTab <table>
Not supported for custom tracks
Auxiliary table with likelihood of variant damage to proteins from SIFT.
Example of a Personal Genome SNP track
track mySnps
type pgSnp
...
A personal genome SNPs track displaying single
nucleotide polymorphisms from the reference genome.
type altGraphX
Alternate slicing gene models specialized track
used to show genome coverage.
Example of an altGraphX track
track sibTxGraph
shortLabel SIB Alt-Splicing
type altGraphX
url http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?species=H.+sapiens&tromer=$$
urlLabel SIB link:
idInUrlSql select name from sibTxGraph where id=%s
...
The Swiss Institute of Biology's
alternative splicing track provides an external link via the url
setting. But the actual "tromer" term in the value
will be filled in with the results of a query to the sibTxGraph
table. With enough obscure settings, the Browser accomplishes
subtle things.
type bedDetail <#>
Extended bed type
format that has a text description embedded in the table for each
item. The format can vary between 4 and 12 standard bed columns
plus two additional ones. The number of columns (including the 2
bedDetail specific columns) must follow the "bedDetail
" term in
the type setting.
Example can be found below.
Example of a bedDetail track
track microattrLoci
type bedDetail 14
itemRgb on
url http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&sendto=t&extrafeatpresent=1&list_uids=$$
...
This bedDetail contains details for each item
formatted for HTML display. In addition each item has an "id" as
distinct from the "name" and that id is used in the outside link
url displayed in the item details page.
type clonePos
A specialized track used to show genome
coverage.
Example of a clonePos track
track clonePos
shortLabel Coverage
longLabel Clone Coverage/Fragment Position
type clonePos
altColor 180,180,180
...
The Coverage track for the human genome will
vary in color between black and light gray, based upon the cloned
sequence coverage depth.
type ctgPos
A specialized track used to show the locations
of contigs on the physical map.
Example of a ctgPos track
track ctgPos2
shortLabel GRC Map Contigs
type ctgPos
url none
...
The GCR Map Contigs track would normally
generate a URL to NCBI, but in this case, the URL has been
explicitly blocked.
type downloadsOnly
A specialized track
that provides access to a set of downloadable files, and is
currently ENCODE only. A downloadsOnly type track does not get
visualized in the Browser.
Example can be found below.
fileSortOrder ...
The fileSortOrder setting is required for
downloadsOnly type tracks. A complete description can be found in
composite tracks section of this document. It requires each file
to be defined as an object in the metaDb and each of those objects
to refer to a "composite" which will be the name of this track and
the directory name where the files are located. The
"fileSortOrder
" defines the column and default sort order. The
user will be able to sort and filter the list of files.
Example of a Downloads Only track
track wgEncodeUmassWengTfbsValid
type downloadsOnly
fileSortOrder cell=Cell_Line \
dccAccession=UCSC_Accession \
fileSize=Size \
fileType=File_Type \
dateSubmitted=Submitted \
dateUnrestricted=RESTRICTED<BR>Until
wgEncode 1
...
The Browser will not provide visualization of
this track but will provide access to downloading any number of
files organized into a single group. The downloads page
presents those files in a table with a number of columns that are
sortable and possibly filterable. Much of the presentation and
organization relies upon settings established in the metaDb for
this track. However, the fileSortOrder
setting has requested six
specific columns to be presented in the desired order.
type encodeFiveC
A specialized track that was used to show the
locations where chromatin may have interactions with other
chromatin locations.
interTable <tableName>
Each location found in the track's main table
should have associated regions defined in the interactions table
named with this setting. The interactions table format
is essentially a "bed 7 + 1".
interTableKind <label>
The table of interactions is presented on each
item's details page and is titled as "Top ___ interactions"
Example of an encodeFiveC track
track encodeUw5cGM06990dS9013DhsLoci
type encodeFiveC
color 200,100,0
interTable encodeUw5cGM06990dS9013DhsInter
interTableKind TSS
...
This Five C interactions track will be
displayed as colored items. The associated chromatin regions are
drawn from a second table. The kind of associations are
transcription start sites.
type factorSource
A bed 15 based table
format with overlapping items. This is a specialized track type
designed for holding transcription factor binding evidence across
multiple cell lines. The format is the same as used for
microarray expression.
Example can be found below.
sourceTable <table>
The factorSource type tracks need a secondary
table that holds descriptions of the sources. This is where cell
line abbreviations are declared and associated with actual cell
lines.
inputTrackTable <table>
When viewing the details for a factorSource
track item (typically a TF binding site), additional information
about the cell line evidence can be displayed. This setting names
a table that will hold the additional information. It is used in
conjunction with the inputTableFieldDisplay
setting.
inputTableFieldDisplay <f1> [f2...]
If there is an inputTrackTable
defined with
your track, the fields that are to be displayed should be declared
with this associated setting.
filterBy <field1:title=[+]option1a...>
[field2:title=[+]opt2a...]
This setting provides user filtering of factorSource items by factor name.
The simplest use is to include a comma-separated list of all factor names in the track as
an argument to the setting.
A complete description of this setting can be found in the
bed/bigBed item-based track settings.
motifTable <table>
A bed 6
table that holds motif regions
to highlight within factorSource items.
motifMapTable <table>
If motif names differ from or are not unique for factorSource item names
in the motifTable
, this table can used to remap the names.
This table has a simple 2 column format: char(255) factor, char(255) motif.
motifPwmTable <table>
When viewing the details of a factorSource track item containing
a binding motif in the motifTable
, the
consensus motif sequence and sequence logo image can be displayed.
This setting names the table holding the position weight matrices
that provide this information.
motifMaxWindow <integer>
Display of highlighted motifs in a factorSource track can be limited using
this setting. In large genomic regions motifs are not well distinguished in
the display, and performance is improved by suppressing the feature.
motifDrawDefault <on/off>
If a factorSource track has a motifTable, this setting controls whether motifs
are drawn by default. It is also configurable by the user.
Example of a factorSource track
track tfbsByCellLines
type factorSource
sourceTable myCellLines
inputTrackTable myCellLineAssociations
inputTableFieldDisplay cellType treatment lab
motifTable transfacMotif
motifPwmTable transfacMotifPwm
motifMapTable transfacMotifTarget
motifMaxWindow 30000
motifDrawDefault on
...
This track will show transcription factor (TF)
binding evidence found in multiple cell lines. Each item represents
a particular TF, along with the cell lines that show
evidence of binding in that location. The secondary sourceTable
holds the definitions of each cell line abbreviation. A third
table is declared with inputTrackTable
and carries details for
each cell line that should be seen in the Browser. When viewed in
item detail, 3 fields (cellType, treatment and lab) will be seen
for each cell associated with the particular TF binding location.
type rmsk
The repeat masker
tracks contain uniquely formattted data for the special function
of repeat-masking.
Example can be found below.
Example of a Repeat Masking track
track rmsk
spectrum on
type rmsk
maxWindowToDraw 10000000
...
The repeat masker track will have individual
repeat items shaded by a measure of how exact a repeated element
is withing the stretch of repetition. This track is restricted to
display at less than 10 million base resolution.
type snake <db>
otherDb <otherDb>
A specialized track
used to show the path of snaking alignments that represent
chromosomal rearrangements, duplications and inversions. Since
this type is almost always a mapping between two species or two
assemblies of the same species, the type must also declare that
species/assembly by database name.
As with chains and netAligns, which typically show mappings between two assemblies,
the "otherDb
" setting is also needed to declare which other genome and assembly
the data in this track represents.
Example of a snake track
track snakeMm9
type snake mm9
otherDb mm9
color 100,50,0
altColor 255,240,200
spectrum on
...
This snake track will illustrate chromosome
rearrangements that have occurred on the mouse mm9 genome as seen
when it is aligned to the human genome.
group <groupId>
All tracks belong to
one of several groups. Hub tracks belong to the group that
encompasses their hub. Other tracks belong to one of the
predefined groups. For hg19 the following groups are defined:
map
- "Mapping and Sequence"
phenDis
- "Phenotype and Disease Associations"
genes
- "Genes and Gene Prediction"
rna
- "mRNA and EST"
expression
- "Expression"
regulation
- "Regulation"
compGeno
- "Comparative Genomics"
neandertal
- "Neandertal Assembly and Analysis"
varRep
- "Variation and Repeats"
If no group is set for a built-in track, then the track will end up
in the Experimental Tracks section at the bottom.
Example of a track belonging to a predefined group
track myTrack
group regulation
...
superTrack on
To declare a supertrack, simply add this
setting to a track definition that will hold a few standard
settings. To set a supertrack to display as default add the word show,
superTrack on show
, to the end of the statement.
When attempting to debug visibility settings, it may be
helpful to read the note about
inheritance found below.
parent <superTrack>
Membership in a supertrack, composite, or aggregate track is declared by the
child, not the supertrack itself. Any number of children may
belong to one supertrack, but ten is a suggested maximum number for usability
considerations. Stylistically, children's stanzas within the trackDB typically are indented
directly under the stanza of the parent. However, this is less frequently the case with
supertracks, because the children are often scattered in other places within the trackDb
file, or the supertrack children are themselves composites containing
additional indentation that makes enforcement of the supertrack
indentation impractical.
Example of a Supertrack
track myFolder
superTrack on
group regulation
shortLabel My Folder
longLabel My folder keeps my tracks together
...
track myFirstTrack
parent myFolder
visibility dense
...
track mySecondTrack
parent myFolder
visibility hide
...
The supertrack called "My Folder"
contains two children. All will be grouped under
"regulation". Notice that the first track is visible by
default (if the supertrack itself is visible), but the second
track is not.
Composite Tracks
Composite tracks are
another level of hierarchy and are meant to group very similar tracks
(called "subtracks") together such that they can all
share the same configuration settings. In its simplest form a
composite holds tracks all of the same type (such as bigBed).
Initially, all track within the set are configured identically.
Usually only some of the subtracks are visible by default, and these
will have the same display mode (e.g., dense
)
and optional settings (e.g., viewLimits
).
While default settings cover the entire composite of related tracks,
in most cases individual subtracks can be configured by the user
independently of the composite settings. However, once individual
subtrack settings are made, they can be overridden by new choices made at
the composite level. It may be helpful to read the "Note about
inheritance" found below.
compositeTrack on
To declare a composite, simply add this setting
to a track definition, along with a few standard settings.
The subtrack stanzas always follow immediately after the
composite track delaration and are indented from it.
Note that since children of composites inherit their parent's
settings, many more trackDb settings will be found at the
composite level than at the supertrack level.
parent <composite> [off/on]
Membership in a composite is declared by the
subtrack child, not the composite itself, through this setting. Any number of subtracks may
belong to one composite, but display performance degrades significantly beyond a
few hundred. Set the parent
setting to "on" to
indicate whether a subtrack should be visible (checked, selected) by default.
Visibility settings in composite subtracks are directly inherited from the parent. Therefore,
any visibility lines added at the child subtrack level of a composite will be ignored.
allButtonPair on
When a simple composite track presents a short list of
subtracks, it can be convenient for the user to have an easy way to select or
deselect all of them. Include this setting to display an "All

"
(plus and minus button pair) for the user's convenience. If
the list contains more than 10 subtracks, other methods may be
more useful for organizing and selecting subtracks (described below).
centerLabelsDense <off/on>
By default, only the composite track's single center label is shown when the
subtracks are displayed together in the Browser dense mode.
If centerLabelsDense
is set to "on", the Browser will display a center
label for each subtrack.
dragAndDrop subTracks
When you have many subtracks in a composite track, it may be useful on the
Track Setting page, also known as the hgTrackUi configuration page, to rearrange
the subtracks. One avenue of rearranging many subtracks is to employ the
sortOrder setting, as described below,
or by allowing the user to drag and drop the subtracks to a new order
on the Track Setting page. The dragAndDrop subTracks
setting will enable
dragging by clicking on the check mark next to the subtrack on the configuration page.
Tracks can thereby be rearranged into a final desired order, that will then be seen when
browsing the tracks. However, the order of tracks can also be rearranged on the hgTracks
Browser image by directly dragging and dropping the displayed track data. Yet reordering subtracks
in the Browser image in hgTracks will not be reflected back on the hgTrackUi configuration page.
Note: This setting will not work correctly if 'container multiWig' is specified.
Example of a Composite track
track myComposite
compositeTrack on
parent myFolder
shortLabel My Composite
type bigWig 0 1.0
viewLimits 0.0:0.2
allButtonPair on
...
track myFirstSubtrack
parent myComposite on
...
track mySecondSubtrack
parent myComposite
...
The composite with two subtracks shown. All
subtracks are of type bigWig and all have a default viewLimits
of 0 - 0.2.
Notice the first subtrack is checked by default, but the second is not
(parent
setting). However, the Browser will display two buttons
(allButtonPair
setting) that allow the user to
select all subtracks, or deselect all of them and then check only those of
interest.
subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a>
[mTag1b=mTitle1b…]
subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a>
[mTag2b= mTitle2b…]
Up to 9 subgroups may be declared, one per line. Each subgroup declaration
must include a whitespace-delimited tag, title, and one or more tag/title
membership pairs joined by an '=
' equals sign.
-
tag
: Used in the code to select
and sort subtracks based upon their membership. Tag names
must be alphanumeric, begin with a letter, not contain a period, and be formed
such that the desired sort order of the member subtracks will result.
-
title
: Label of the subgroup as it appears on the
selection matrix that is displayed to the user, e.g.,"Antibody". Spaces within
titles must be replaced by '_
'. A limited amount
of HTML is allowed in titles, such as the insertion of Greek letters using an HTML
code. Any use of HTML should be tested to ensure that it displays correctly.
Because subgroup settings are often lengthy, it is recommended that the
'\
' line continuation character be used to break up the setting over
multiple lines for easier reading.
subGroups <gTag1=mTag1?> [gTag2= mTag2?]
The subtracks themselves declare their
membership in a group with the subGroups
setting.
Each subtrack must declare its membership in all of its
composite's subgroups. Notice that membership is declared
by pairs of tags: the group tag (e.g. gTag1) is paired with that
group's member tag (e.g. mTag1b) as gTag1=mTag1b (cell=K562).
dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]
In order to define the type of UI desired for
selecting subtracks based upon groups, additional settings are
needed at the composite level. For a one- or two-dimensional array of
checkboxes, declare the dimensions X and Y. Additional dimensions (called
"abc") can be declared with this setting as dimA, dimB, etc.
Note that the order of the subgroups in a dimension is exactly the same as
the order they appear in the subGroup#
setting, regardless of whether
the subtrack list is sorted by tags.
filterComposite <dim[A/B/C][=one]> [dimB dimC ...]
For the "abc"
dimensions, rows of checkboxes will be shown by default. However, this
UI can be confusing, especially combined with a one- or two-dimensional matrix.
Instead, it is recommended that you organize "abc"
dimensions as drop-down multi-selects, often referred to as
"filter" boxes due to their similarity to the
filterBy
setting discussed
above. Declare the subtrack filter boxes with the filterComposite
setting. Filter composites may work with or without the X/Y
matrix, but are restricted to the "abc" dimensions.
By default, the filter box for selecting
subtracks is multi-select, meaning more than one choice is
allowed. It is possible to restrict this to a single choice by
adding the "=one
" option to the filter box definition.
This might make sense when there are only 2 choices. The choice
of "all" is always available, while choosing nothing is an invalid
case.
dimension<?>checked <mTag1a>
[mTag1b …]
One more complication in the selection process is
determining which subgroup options are selected by default. In the
case of the X/Y matrix this can be determined by what subtracks
are currently checked. But, "abc" dimensions must have their
selected state declared explicitly using the
dimension<?>checked setting.
controlledVocabulary <pathToFile> <gTag#=mdbVar>
[gTag#=mdbVar …]
NOT FOR HUBS. Currently used only by ENCODE
In ENCODE, subgroups
are often based on metadata terms declared in the metaDb table and defined
in the "controlled vocabulary", which is
stored as an ra file. In this situation, the labels of these
terms, as they are displayed in the track configuration page, can
be linked to the controlled vocabulary definitions. These links
can be quite useful, as the term definition may include protocol
documents and validation evidence. In order to establish the
links, each subGroup's tag must be tied to the actual metaDb
term.
sortOrder <gTag#=+/-> [gTag#=- …]
When declaring subgroups, it is often useful to
sort the subtrack list by those subgroups. By including a
sortOrder setting, long sets of subtracks are more easily
organized and navigated by the user. If there are only a few
subtracks in the composite, sorting may be of little value and
dragAndDrop may be a better option.
Currently only subgroups can be defined in the sortOrder, but it
is anticipated that this will expand to include short and long
labels as well. Sorting will occur on the tag values defined in the
subGroup#
and subGroups
settings. By sorting
on tags, non-alphanumeric orders can be defined.
fileSortOrder <var=val> [var=val ...]
NOT FOR HUBS. Currently used only by ENCODE
Some composite track sets have their own
directories of downloadable files and a special CGI for accessing
those files. In order to see the CGI interface for the download
directory, the composite needs an object for each file defined in
the metaDb. The trackDb stanza for the composite also needs to
have the fileSortOrder setting defined. The setting is defined as
a set of variable=value pairs, which defines the default sort
order on metaDb variables. The "var" portion of the each pair is
a term defined in the metaDb for all of the file objects in the
directory. The "var" may also be "fileType
" or "fileSize
",
which are not defined in the metaDb. The "val" is the title that the
user will see as the column header for the sortable table of
files. This value can contain and '_
' for spaces and limited HTML
codes and special characters. As always, you are encouraged to
experiment. The '\
' continuation character should be used to
break up this long setting into readable lines.
Examples of Composite tracks with Subgroups
track myComposite
compositeTrack on
subGroup1 cellLine Cell_Line \
A1GM12=GM12878 \
CD14=CD14+ …
subGroup2 ab Antibody \
H3K04ME3=H3K4me3 \
H3K36ME3=H3K36me3 …
dimensions dimX=ab dimY=cellLine
sortOrder cell=+ ab=+
...
track myFirstSubtrack
parent myComposite on
subGroups cellLine=CD14 ab=H3K04ME3
...
This examples shows a composite with
one subtrack and two subgroups. The
dimensions setting declares X and Y dimensions, which will display
a 2D matrix on the composite's configuration page. Notice that the
title of the cellLine subgroup contains a blank space filled in
with '_
'. The second cell line, "CD14+", includes an HTML encoding
for '+
' in its title, The two subgroups participate in the default
sort order of subtracks, but they each have non-standard sort orders. In the
cellLine subgroup, GM12878 sorts first by starting its tag with "A". The
antibodies have numbers in their titles, but the tags expand
the number with "0" to pad the spacing. This ensures
H3K4me3 sorts before H3K36me3.
track myCompositeIs3D
compositeTrack on
subGroup1 cellLine Cell_Line \
A1GM12=GM12878 \
CD14=CD14+ …
subGroup2 ab Antibody \
H3K04ME3=H3K4me3 \
H3K36ME3=H3K36me3 …
subGroup3 treat Treatment \
TNFA=TNF-alpha \
ZNONE=None …
dimensions dimX=ab dimY=cellLine dimA=treat
filterComposite dimA
dimensionAchecked ZNONE
controlledVocabulary encode/cv.ra cellLine=cell \
ab=antibody \
treat=treatment
sortOrder cell=+ ab=+ treat=-
fileSortOrder cell=Cell_Line \
antibody=Antibody \
fileSize=Size
...
track myFirstSubtrackIn3D
parent myCompositeIs3D on
subGroups cellLine=CD14 ab=H3K04ME3 treat=ZNONE
...
In this second example composite,
one subtrack and three subgroups are shown. As in the previous example, the
dimensions setting declares X and Y dimensions, resulting in
a 2D matrix of "Antibody" and "Cell Line" options. A third "Treatment" subgroup is
declared as the "A"
dimension; the user will be able to select subtracks for this
dimension via a dropdown multi-select filter box. All three subgroups
participate in the default sort order of subtracks, and the treatment subgroup is
sorted in reverse order by default. The "None" treatment
sorts before all others (in reverse order) by beginning the tag with
a "Z". Note that for this "A" dimension,
the "None" treatment will be selected by default. By
declaring the proper settings, using subGroups to organize a
composite can be quite powerful.
This example illustrates that
subgroups, dimensions, and (in the case of ENCODE) controlled vocabulary and
metadata all must be linked together for the composite to fully
work. Further, the actual terms, programmatic "tags"
and user visible titles all have different constraints and roles
to play in establishing this cohesion. Subgroup tags are used to
organize subtracks, while lettered dimensions organize the
configuration page to more easily select subgroups of subtracks.
For ENCODE tracks, the subgroups may be represented as metadata
"terms" (distinct from tags) that are often carefully
defined by a controlled vocabulary. In the example above, the tag
"ab" is used to organize subtracks into subgroups but
is also tied to dimension X. This ensures that antibodies will
appear as the horizontal dimension in the 2D matrix on the
configuration page, and the selection of an antibody will select the
associated subtracks. Of course the user does not see the
antibody as "ab" but "Antibody". Going
further, the term as defined in controlled vocabulary is
"antibody", so that for all the tables and files
associated with this composite track, their metaDb objects should
contain an "antibody" var and a given antibody (e.g.
H3K4me3) will be found in the controlled vocabulary with a
validation document. All the relationships can be confusing, but
the trackDb settings, if done correctly, can tie all these
elements together in a nice cohesive package.
Examples of Composite tracks with Subgroups
track myComposite
compositeTrack on
subGroup1 cellLine Cell_Line \
A1GM12=GM12878 \
CD14=CD14+ …
subGroup2 ab Antibody \
H3K04ME3=H3K4me3 \
H3K36ME3=H3K36me3 …
dimensions dimX=ab dimY=cellLine
sortOrder cell=+ ab=+
...
track myFirstSubtrack
parent myComposite on
subGroups cellLine=CD14 ab=H3K04ME3
...
This examples shows a composite with
one subtrack and two subgroups. The
dimensions setting declares X and Y dimensions, which will display
a 2D matrix on the composite's configuration page. Notice that the
title of the cellLine subgroup contains a blank space filled in
with '_
'. The second cell line, "CD14+", includes an HTML encoding
for '+
' in its title, The two subgroups participate in the default
sort order of subtracks, but they each have non-standard sort orders. In the
cellLine subgroup, GM12878 sorts first by starting its tag with "A". The
antibodies have numbers in their titles, but the tags expand
the number with "0" to pad the spacing. This ensures
H3K4me3 sorts before H3K36me3.
track myCompositeIs3D
compositeTrack on
subGroup1 cellLine Cell_Line \
A1GM12=GM12878 \
CD14=CD14+ …
subGroup2 ab Antibody \
H3K04ME3=H3K4me3 \
H3K36ME3=H3K36me3 …
subGroup3 treat Treatment \
TNFA=TNF-alpha \
ZNONE=None …
dimensions dimX=ab dimY=cellLine dimA=treat
filterComposite dimA
dimensionAchecked ZNONE
sortOrder cell=+ ab=+ treat=-
...
track myFirstSubtrackIn3D
parent myCompositeIs3D on
subGroups cellLine=CD14 ab=H3K04ME3 treat=ZNONE
...
In this second example composite,
one subtrack and three subgroups are shown. As in the previous example, the
dimensions setting declares X and Y dimensions, resulting in
a 2D matrix of "Antibody" and "Cell Line" options. A third "Treatment" subgroup is
declared as the "A"
dimension; the user will be able to select subtracks for this
dimension via a dropdown multi-select filter box. All three subgroups
participate in the default sort order of subtracks, and the treatment subgroup is
sorted in reverse order by default. The "None" treatment
sorts before all others (in reverse order) by beginning the tag with
a "Z". Note that for this "A" dimension,
the "None" treatment will be selected by default. By
declaring the proper settings, using subGroups to organize a
composite can be quite powerful.
subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b…]
track <viewName>
view <viewTag>
A view is always declared both as a subgroup
and in a track stanza itself. The subgroup declaration is like
previous declarations, but the view subgroup must have the tag
view
and be declared as the first subgroup. Note
that the view stanza follows the composite stanza with one level
of indentation. Subtracks will follow their view with an
additional level of indentation.
subGroups view=<vTag1>…
parent <viewName> [off/on]
A subtrack declares its membership in a view
both as subgroup membership and with a parent setting that refers
to the view track name. Note that a track can only have one parent.
When the subtrack's parent is a view, the composite track is
its implicit grandparent.
viewUi on
If subtracks within a view are configurable,
then the view will have the configuration controls for it in a box
beneath the view's visibility drop down. That box filled with
configuration controls is hidden by default so that the UI is not
too cluttered. The user must first open the box before its
contents are seen. If there is only one view with configuration
settings, or if the view is the most important one, the box can be
open by default. Use this setting in the view stanza of settings
to default the configuration box as open.
configurable <off/on>
Tracks are configurable by default if their
track type supports this, and views and composites are
configurable if their children's track type supports this.
Finally individual subtracks are configurable by default
if their track type supports it. Sometimes it is desirable
to turn off configuration. Configuration may be turned back
on when it has been turned off at a higher level. For example, this might be
useful in a situation with a multi-view composite where the composite
level would normally be configurable, but you want only one of the
views and not all of the children of that view to be configurable.
While this setting might be rarely needed, it can help restrict
the user from viewing your data in inappropriate ways.
Example of a Composite track with Views
track myMultiViewComposite
compositeTrack on
visibility dense
subGroup1 view Views PK=Peaks SIG=Signals
subGroup2 cell Cell_Line \
A1GM12=GM12878 \
CD14=CD14+ …
subGroup3 ab Antibody \
H3K04ME3=H3K4me3 \
H3K36ME3=H3K36me3 …
dimensions dimX=ab dimY=cell
sortOrder cell=+ ab=+ view=+
type bed 3
...
track myViewPeaks
parent myMultiViewComposite
shortLabel Peaks
view PK
visibility pack
type bigBed 6 +
scoreFilter 0
scoreFilterLimits 0:1000
viewUi on
...
track myFirstPeakSubtrack
parent myViewPeaks on
subGroups cell=CD14 ab=H3K04ME3 view=PK
...
The composite has two views, one of which is
shown, along with a single subtrack belonging to that view.
Notice that the view does not participate in the dimensions
setting, as it is an implicit dimension controlled by a row of
visibility dialogs at the top of the composite configuration page.
Notice that the view does participate in the sortOrder setting
like other subgroups. In this example, the peaks view contains
bigBed subtracks that all share the scoreFilter defaults
defined at the view level. Almost any setting that is common to
the whole tree can be defined at the composite level; any setting
that is common to the view can be set at the view level; and any
setting that is specific to one subtrack should be set at that
level. Remembering inheritance, we
can see that the subtrack shown inherits its track type from
the view, but has its default visibility limited by the composite.
That is, it inherits packed visibility from the view but the
composite will show all visible subtracks as dense.
One additional thing to note is that this composite track is
"type bed 3
". Composites do not need a type to define
their data format, since all data is associated with subtracks. Further,
multi-view composites almost always have multiple data formats.
But the "type" also controls what configuration options may be offered
for a track. Typically, a single level composite has the same type as
all of its subtracks and offers user configuration options at the top
level. But a multi-view composite is most often given the bare-bones
"type bed 3
", and offers user configuration options at
the view level. Exceptions to this pattern do exist but they are rare.
container multiWig
Signal overlay tracks are declared much like
simple composites. However, instead of a "composite"
setting, they declare themselves as a "container" of
"type multiWig
". Like simple composites, all subtrack
types should be identical and the container itself should be
declared as the same type (e.g. "bigWig
"). Also like a composite,
the container parent should have common settings for all children.
Unlike composites, containers can have neither subgroups nor
views. Additionally, all subtracks within a container are configured as one;
there is no independent configuration of individual subtracks. Even when the user
sets the overlay method to none and the subtracks are viewed as
separate signals, they are still configured as a set.
parent <containerTrack>
Membership in a container track is declared at
the subtrack level. The subtracks should be defined with indent
beneath their container parent.
aggregate <transparentOverlay/stacked/solidOverlay/none>
It is important to declare an aggregation method; otherwise, this set of tracks displays
as a composite would, with additional restrictions. Of the four options, the preferred
setting is transparentOverlay
. The setting stacked
will draw the graphs in stacked mode.
The setting solidOverlay
should not be used if there
are more than a couple of tracks, and none
should never be the
default. The aggregation method is a configurable option,
however, so the user may wish to temporarily set it to none in
order to see subtleties hidden in overlay mode.
showSubtrackColorOnUi on
Subtracks in an overlay have individual colors. Use this setting to show the color
associated with each on the track configuration page.
Example of an Aggregate track
track myMultiWig
container multiWig
aggregate transparentOverlay
showSubtrackColorOnUi on
type bigWig 0 1000
viewLimits 0:10
maxHeighPixels 100:32:8
...
track myFirstOverlaySig
table myFirstWig
parent myMultiWig
color 255,128,128
wig 0 1139
...
track myFirstBigWig
parent myMultiWig
color 120,235,204
...
This container is for a transparent overlay of
signal tracks with 2 subtracks shown. The tracks are
of type "bigWig
", though the first subtrack is a wig
.
Such mixtures are allowed. Notice that the wig has a slightly
larger range than the others. The signal dimensions are close
enough in this case, and the default viewLimit applied to all
subtracks suggests that any signal above 10 is interpreted as
strong. Note that each subtrack must define its color, and
in this example, that color will be seen in the track
configuration page as well as in the image. Also notice that the
first subtrack declares a table as distinct from its track name.
Usually the table (or remote file root) name is the same as the
track name. The track name is a unique key. But it is frequently
the case that a table or remote data file may be displayed as an
individual track or subtrack, as well as part of a signal overlay
track. Setting the table name here suggests that a track named
"myFirstWig" also exists and is displaying the same data used in
this overlay track.
Example of an Aggregate track
track myMultiWig
container multiWig
aggregate transparentOverlay
showSubtrackColorOnUi on
type bigWig 0 1000
viewLimits 0:10
maxHeighPixels 100:32:8
...
track myFirstOverlaySig
parent myMultiWig
color 255,128,128
type bigWig 0 1139
...
track myFirstBigWig
parent myMultiWig
color 120,235,204
...
This container is for a transparent overlay of
signal tracks with 2 subtracks shown. The tracks are
of type "bigWig
". Notice that the first subtrack has a slightly
larger range than the others. The signal dimensions are close
enough in this case, and the default viewLimit applied to all
subtracks suggests that any signal above 10 is interpreted as
strong. Note that each subtrack must define its color, and
in this example, that color will be seen in the track
configuration page as well as in the image.
genome
Filled with genome/assembly db name.
offset
Used only once, to apply an offset to bed
type data of a custom track.
browserLines
Internal only – user does not set.
Filled with all trackDb.ra style lines from
hgCustom input.
dataUrl
Internal only – user does not set.
Filled if custom tracks is loaded via URL.
dbTrackType
Internal only – user does not set.
Not sure how it is distinguished from
tdbType.
fieldCount
Internal only – user does not set.
Filled with number of bed columns as
determined in hgCustom CGI.
firstItemPos
Internal only – user does not set.
Filled with first bed item in bedList in
hgCustom CGI.
htmlFile
Internal only – user does not set.
Filled with name if trash file that contains
HTML description for custom track.
htmlUrl
Internal only – user does not set.
Filled with user entered URL for track
description in hgCustom CGI.
initialPos
Internal only – user does not set.
Filled with position from hgCustom input.
inputType
Internal only – user does not set.
Filled with custom factory name as
determined in hgCustom CGI.
itemCount
Internal only – user does not set.
Filled with bed item slCount in hgCustom
CGI.
mafFile
Internal only – user does not set.
Filled with name of trash file that contains
maf data as loaded in hgCustom CGI.
maxChromName
Internal only – user does not set.
Obsolete: Filled with minimum index size for
db that won't "smoosh" together chromNames.
origTrackLine
Internal only – user does not set.
Filled with "track" line as entered by user
in hgCustom CGI.
tdbType
Internal only – user does not set.
Holds the type that should go into
tdb->type.
wibFile
Internal only – user does not set.
Filled with name of trash file that contains
wib binary data as loaded in hgCustom CGI.
wigFile
Internal only – user does not set.
Filled with name of trash file that contains
wig data as loaded in hgCustom CGI.