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The bigWig format is the recommended format for almost
all graphing track needs (for more information, see the following
wiki page). The wiggle (WIG) format is an older format for
display of dense, continuous data such as GC percent, probability scores, and
transcriptome data. Wiggle data elements must be equally sized. The
bedGraph format is also an older format used to display
sparse data or data that contains elements of varying size.
For speed and efficiency, wiggle data is compressed and stored internally in
128 unique bins. This compression means that there is a minor loss of precision
when data is exported from a wiggle track (i.e., with output format
"data points" or "bed format" within the table browser).
The bedGraph format should be used if it
is important to retain exact data when exporting.
General Structure Wiggle format is line-oriented. For wiggle custom
tracks, the first line must be a track definition line (i.e., track type=wiggle_0), which
designates the track as a wiggle track and adds a number of options for
controlling the default display.
Wiggle format is composed of declaration lines and data lines, and require a
separate wiggle track definition line. There are
two options for formatting wiggle data: variableStep and fixedStep.
These formats were developed to allow the file to be written as compactly as
possible.
- variableStep is for data with irregular intervals between new
data points and is the more commonly used wiggle format. After the wiggle
track definition line, variableStep begins with a
declaration line and is followed by two columns containing chromosome positions
and data values:
variableStep chrom=chrN [span=windowSize]
chromStartA dataValueA
chromStartB dataValueB
... etc ... ... etc ...
The declaration line starts with the word variableStep and is followed
by a specification
for a chromosome. The optional span parameter (default: span=1)
allows data composed of contiguous runs of bases with the same data value
to be specified more succinctly. The span begins at each chromosome position
specified and indicates the number of bases that data value should cover.
For example, this variableStep specification:
variableStep chrom=chr2
300701 12.5
300702 12.5
300703 12.5
300704 12.5
300705 12.5
is equivalent to:
variableStep chrom=chr2 span=5
300701 12.5
Both versions display a value of 12.5 at position 300701-300705 on
chromosome 2.
Caution for sparse variableStep data
The wiggle format was designed for quickly displaying data that is quite
dense. The variableStep format, in particular, becomes very inefficient when
there are only a few data points per 1,024 bases. If variableStep data points
(i.e., chromStarts) are greater than about 100 bases apart, it is
advisable to use BedGraph format.
- fixedStep is for data with regular intervals between new data
values and is the more compact wiggle format. After the wiggle track
definition line, fixedStep begins with a declaration
line and is followed by a single column of data values:
fixedStep chrom=chrN start=position step=stepInterval [span=windowSize]
dataValue1
dataValue2
... etc ...
The declaration line starts with the word fixedStep and includes
specifications for chromosome, start coordinate, and step size. The
span specification has the same meaning as in variableStep format.
For example, this fixedStep specification:
fixedStep chrom=chr3 start=400601 step=100
11
22
33
displays the values 11, 22, and 33 as single-base regions on chromosome 3
at positions 400601, 400701, and 400801, respectively. Adding span=5 to the
declaration line:
fixedStep chrom=chr3 start=400601 step=100 span=5
11
22
33
causes the values 11, 22, and 33 to be displayed as 5-base regions on
chromosome 3 at positions 400601-400605, 400701-400705, and 400801-400805,
respectively.
Note that for both variableStep and fixedStep formats, the same span must be
used throughout the dataset. If no span is specified, the default span of 1
is used.
As the name suggests, fixedStep wiggles require the same size step throughout
the dataset. If not specified, a step size of 1 is used.
Data Values
Wiggle track data values can be integer or real, positive or negative values.
Chromosome positions are specified as 1-relative. For a chromosome of length
N, the first position is 1 and the last position is N. Only positions
specified have data. Positions not specified do not have data and will not
be graphed. All positions specified in the input data must be in numerical
order.
Parameters for custom wiggle track definition lines
All options are placed in a single line separated by spaces:
track type=wiggle_0 name=track_label description=center_label visibility=display_mode color=r,g,b altColor=r,g,b priority=priority autoScale=on|off alwaysZero=on|off gridDefault=on|off maxHeightPixels=max:default:min graphType=bar|points viewLimits=lower:upper yLineMark=real-value yLineOnOff=on|off windowingFunction=mean+whiskers|maximum|mean|minimum smoothingWindow=off|2-16
The track type with version is REQUIRED, and it currently must be wiggle_0:
type wiggle_0
The remaining values are OPTIONAL:
name <trackLabel> # default is "User Track"
description <centerLabel> # default is "User Supplied Track"
visibility <full|dense|hide> # default is hide
color <RRR,GGG,BBB> # default is 255,255,255
altColor <RRR,GGG,BBB> # default is 128,128,128
priority <N> # default is 100
For a list of additional options, see the bigWig format page.
Examples
This example specifies 19 separate data points in two tracks in the region
chr19:49,304,200-49,310,700. To view this example as a custom track in the
Genome Browser, copy the text and paste it
into the "Add Custom Tracks" text box.
browser position chr19:49304200-49310700
browser hide all
# 150 base wide bar graph at arbitrarily spaced positions,
# threshold line drawn at y=11.76
# autoScale off viewing range set to [0:25]
# priority = 10 positions this as the first graph
# Note, one-relative coordinate system in use for this format
track type=wiggle_0 name="variableStep" description="variableStep format" visibility=full autoScale=off viewLimits=0.0:25.0 color=50,150,255 yLineMark=11.76 yLineOnOff=on priority=10
variableStep chrom=chr19 span=150
49304701 10.0
49304901 12.5
49305401 15.0
49305601 17.5
49305901 20.0
49306081 17.5
49306301 15.0
49306691 12.5
49307871 10.0
# 200 base wide points graph at every 300 bases, 50 pixel high graph
# autoScale off and viewing range set to [0:1000]
# priority = 20 positions this as the second graph
# Note, one-relative coordinate system in use for this format
track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points priority=20
fixedStep chrom=chr19 start=49307401 step=300 span=200
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