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Summary
Analysis summary
Summary:
The raw bam files, one for each RNA-Seq sample, were summarized to read counts table, using the Bioconductor package GenomicRanges. In the final read counts table, each row represented each column one RNA-Seq sample and each cell, the corresponding read counts associated with each row and column.The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc.) using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples (5685 genes). The output of the normalization algorithm was a table with normalized counts, which can be used for differential expression analysis with statistical algorithms developed specifically for count data. Prior to the statistical testing procedure, the gene read counts were filtered for possible artifacts that could affect the subsequent statistical testing procedures. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500 (1079 genes), ii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp (0 genes with cutoff value 0.07778 average reads per 100 bp), iii) genes with read counts below the median read counts of the total normalized count distribution (4285 genes with cutoff value 10 normalized read counts). The total number of genes excluded due to the application of gene filters was 2043. The total (unified) number of genes excluded due to the application of all filters was 10309. The resulting gene counts table was subjected to differential expression analysis for the contrasts Byn versus Ras using the Bioconductor package DESeq. The final numbers of differentially expressed genes were (per contrast): for the contrast Byn versus Ras, 1204 (448) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 618 (270) were up-regulated, 585 (178) were down-regulated and 1 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale. Literature references for all the algorithms used can be found at the end of this report.
Read counts file: imported sam/bam/bed files
Conditions: Byn, Ras
Samples included: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3
Samples excluded:
none
Requested contrasts: Byn_vs_Ras
Library sizes:
- YA3R1-Byn1: 1235358
- YA3R2-Byn2: 3176848
- YA3R3-Byn3: 1403255
- YA3R4-BynRas1: 2426974
- YA3R5-BynRas2: 1952347
- YA3R6-BynRas3: 2658557
Annotation: download
Organism:
Annotation source: Ensembl genomes
Count type: utr
Exon filters:
none applied
Gene filters:
length, avg.reads, expression, biotype - avg.reads
- average.per.bp: 100
- quantile: 0.25
- expression
- median: TRUE
- mean: FALSE
- quantile: NA
- known: NA
- custom: NA
- biotype
- pseudogene: FALSE
- lincRNA: FALSE
- protein_coding: FALSE
- antisense: FALSE
- processed_transcript: FALSE
- snRNA: FALSE
- sense_intronic: FALSE
- miRNA: FALSE
- misc_RNA: FALSE
- snoRNA: FALSE
- rRNA: TRUE
- polymorphic_pseudogene: FALSE
- sense_overlapping: FALSE
- three_prime_overlapping_ncrna: FALSE
- TR_V_gene: FALSE
- TR_V_pseudogene: TRUE
- TR_D_gene: FALSE
- TR_J_gene: FALSE
- TR_C_gene: FALSE
- TR_J_pseudogene: TRUE
- IG_C_gene: FALSE
- IG_C_pseudogene: TRUE
- IG_J_gene: FALSE
- IG_J_pseudogene: TRUE
- IG_D_gene: FALSE
- IG_V_gene: FALSE
- IG_V_pseudogene: TRUE
Filter application: after normalization
Normalization algorithm: DESeq
Normalization arguments:
locfunc - [[list(locfunc = function (x, na.rm = FALSE)
standardGeneric("median"))locfunc
Statistical algorithm(s): DESeq
Statistical arguments for DESeq: method, sharingMode, fitType - method: blind
- sharingMode: fit-only
- fitType: local
Meta-analysis method: no meta-analysis, reported p-values from the first supplied statistical algorithm
Multiple testing correction: Benjamini-Hochberg FDR
p-value threshold: 0.05
Logarithmic tranformation offset: 1
Analysis preset: not available
Quality control plots: multidimensional scaling, biotype detection, biotype counts, sample and biotype saturation, filtered biotypes, correlation heatmap and correlogram, pairwise scatterplots between samples, boxplots, GC-content bias, transcript length bias, mean-difference plot, mean-variance plot, DEG biotype detection, volcano plot, DEG heatmap
Figure format: png, pdf
Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347
Output data: Annotation, p-value, Adjusted p-value (FDR), Fold change, Read counts
Output scale(s): log2 scale, Reads per Gene Model
Output values: Normalized values
Output statistics: Mean, Median, Standard deviation, Median Absolute Deviation (MAD), Coefficient of Variation, Robust Coefficient of Variation
Total run time: 03 minutes 42 seconds
Filtered genes
Number of filtered genes: 10309 which is the union of
- Filtered because of zero reads: 5685
-
Filtered because of exon filters: 0
-
Filtered because of gene filters: 4624
which is the union of
- length: 1079 genes with filter cutoff value 500
- avg.reads: 907 genes with filter cutoff value 0.07778481
- expression: 4285 genes further decomposed to (filter name, filtered genes, filter cutoff):
- median: 4285 genes with filter cutoff value 10
- biotype: 56 genes with filter cutoff value rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene
Differentially expressed genes
Number of differentially expressed genes per contrast:
- Byn_vs_Ras: 1204 (448) statistically significant genes of which 618 (270) up regulated, 585 (178) down regulated and 1 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log2 scale.
Run log[ 2017-06-01 17:08:57 ] INFO 2017-06-01 17:08:57: Data processing started... [ 2017-06-01 17:08:57 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 17:08:57 ] INFO Conditions: Byn, Ras [ 2017-06-01 17:08:57 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 17:08:57 ] INFO Samples to exclude: none [ 2017-06-01 17:08:57 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 17:08:57 ] INFO Annotation: download [ 2017-06-01 17:08:57 ] INFO Organism: dm6 [ 2017-06-01 17:08:57 ] INFO Reference source: ensembl [ 2017-06-01 17:08:57 ] INFO Count type: utr [ 2017-06-01 17:08:57 ] INFO Exon filters: none applied [ 2017-06-01 17:08:57 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 17:08:57 ] INFO length: [ 2017-06-01 17:08:57 ] INFO length: 500 [ 2017-06-01 17:08:57 ] INFO avg.reads: [ 2017-06-01 17:08:57 ] INFO average.per.bp: 100 [ 2017-06-01 17:08:57 ] INFO quantile: 0.25 [ 2017-06-01 17:08:57 ] INFO expression: [ 2017-06-01 17:08:57 ] INFO median: TRUE [ 2017-06-01 17:08:57 ] INFO mean: FALSE [ 2017-06-01 17:08:57 ] INFO quantile: NA [ 2017-06-01 17:08:57 ] INFO known: NA [ 2017-06-01 17:08:57 ] INFO custom: NA [ 2017-06-01 17:08:57 ] INFO biotype: [ 2017-06-01 17:08:57 ] INFO pseudogene: FALSE [ 2017-06-01 17:08:57 ] INFO lincRNA: FALSE [ 2017-06-01 17:08:57 ] INFO protein_coding: FALSE [ 2017-06-01 17:08:57 ] INFO antisense: FALSE [ 2017-06-01 17:08:57 ] INFO processed_transcript: FALSE [ 2017-06-01 17:08:57 ] INFO snRNA: FALSE [ 2017-06-01 17:08:57 ] INFO sense_intronic: FALSE [ 2017-06-01 17:08:57 ] INFO miRNA: FALSE [ 2017-06-01 17:08:57 ] INFO misc_RNA: FALSE [ 2017-06-01 17:08:57 ] INFO snoRNA: FALSE [ 2017-06-01 17:08:57 ] INFO rRNA: TRUE [ 2017-06-01 17:08:57 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 17:08:57 ] INFO sense_overlapping: FALSE [ 2017-06-01 17:08:57 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 17:08:57 ] INFO TR_V_gene: FALSE [ 2017-06-01 17:08:57 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 17:08:57 ] INFO TR_D_gene: FALSE [ 2017-06-01 17:08:57 ] INFO TR_J_gene: FALSE [ 2017-06-01 17:08:57 ] INFO TR_C_gene: FALSE [ 2017-06-01 17:08:57 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 17:08:57 ] INFO IG_C_gene: FALSE [ 2017-06-01 17:08:57 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 17:08:57 ] INFO IG_J_gene: FALSE [ 2017-06-01 17:08:57 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 17:08:57 ] INFO IG_D_gene: FALSE [ 2017-06-01 17:08:57 ] INFO IG_V_gene: FALSE [ 2017-06-01 17:08:57 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 17:08:57 ] INFO Filter application: postnorm [ 2017-06-01 17:08:57 ] INFO Normalization algorithm: deseq [ 2017-06-01 17:08:57 ] INFO Normalization arguments: [ 2017-06-01 17:08:57 ] INFO locfunc: [ 2017-06-01 17:08:57 ] INFO [[ [ 2017-06-01 17:08:57 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 17:08:57 ] INFO locfunc [ 2017-06-01 17:08:57 ] INFO Statistical algorithm: deseq [ 2017-06-01 17:08:57 ] INFO Statistical arguments: [ 2017-06-01 17:08:57 ] INFO deseq: blind, fit-only, local [ 2017-06-01 17:08:57 ] INFO Meta-analysis method: none [ 2017-06-01 17:08:57 ] INFO Multiple testing correction: BH [ 2017-06-01 17:08:57 ] INFO p-value threshold: 0.05 [ 2017-06-01 17:08:57 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 17:08:57 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 17:08:57 ] INFO Figure format: png, pdf [ 2017-06-01 17:08:57 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 17:08:57 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 17:08:57 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 17:08:57 ] INFO Output values: normalized [ 2017-06-01 17:08:57 ] INFO Downloading gene annotation for dm6... [ 2017-06-01 17:09:04 ] INFO Downloading transcript annotation for dm6... [ 2017-06-01 17:09:21 ] INFO Converting annotation to GenomicRanges object... [ 2017-06-01 17:09:21 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-06-01 17:21:43 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"... [ 2017-06-01 17:21:43 ] INFO 2017-06-01 17:21:43: Data processing started... [ 2017-06-01 17:21:43 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 17:21:43 ] INFO Conditions: Byn, Ras [ 2017-06-01 17:21:43 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 17:21:43 ] INFO Samples to exclude: none [ 2017-06-01 17:21:43 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 17:21:43 ] INFO Annotation: download [ 2017-06-01 17:21:43 ] INFO Organism: dm3 [ 2017-06-01 17:21:43 ] INFO Reference source: ensembl [ 2017-06-01 17:21:43 ] INFO Count type: utr [ 2017-06-01 17:21:43 ] INFO Exon filters: none applied [ 2017-06-01 17:21:43 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 17:21:43 ] INFO length: [ 2017-06-01 17:21:43 ] INFO length: 500 [ 2017-06-01 17:21:43 ] INFO avg.reads: [ 2017-06-01 17:21:43 ] INFO average.per.bp: 100 [ 2017-06-01 17:21:43 ] INFO quantile: 0.25 [ 2017-06-01 17:21:43 ] INFO expression: [ 2017-06-01 17:21:43 ] INFO median: TRUE [ 2017-06-01 17:21:43 ] INFO mean: FALSE [ 2017-06-01 17:21:43 ] INFO quantile: NA [ 2017-06-01 17:21:43 ] INFO known: NA [ 2017-06-01 17:21:43 ] INFO custom: NA [ 2017-06-01 17:21:43 ] INFO biotype: [ 2017-06-01 17:21:43 ] INFO pseudogene: FALSE [ 2017-06-01 17:21:43 ] INFO lincRNA: FALSE [ 2017-06-01 17:21:43 ] INFO protein_coding: FALSE [ 2017-06-01 17:21:43 ] INFO antisense: FALSE [ 2017-06-01 17:21:43 ] INFO processed_transcript: FALSE [ 2017-06-01 17:21:43 ] INFO snRNA: FALSE [ 2017-06-01 17:21:43 ] INFO sense_intronic: FALSE [ 2017-06-01 17:21:43 ] INFO miRNA: FALSE [ 2017-06-01 17:21:43 ] INFO misc_RNA: FALSE [ 2017-06-01 17:21:43 ] INFO snoRNA: FALSE [ 2017-06-01 17:21:43 ] INFO rRNA: TRUE [ 2017-06-01 17:21:43 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 17:21:43 ] INFO sense_overlapping: FALSE [ 2017-06-01 17:21:43 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 17:21:43 ] INFO TR_V_gene: FALSE [ 2017-06-01 17:21:43 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 17:21:43 ] INFO TR_D_gene: FALSE [ 2017-06-01 17:21:43 ] INFO TR_J_gene: FALSE [ 2017-06-01 17:21:43 ] INFO TR_C_gene: FALSE [ 2017-06-01 17:21:43 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 17:21:43 ] INFO IG_C_gene: FALSE [ 2017-06-01 17:21:43 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 17:21:43 ] INFO IG_J_gene: FALSE [ 2017-06-01 17:21:43 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 17:21:43 ] INFO IG_D_gene: FALSE [ 2017-06-01 17:21:43 ] INFO IG_V_gene: FALSE [ 2017-06-01 17:21:43 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 17:21:43 ] INFO Filter application: postnorm [ 2017-06-01 17:21:43 ] INFO Normalization algorithm: deseq [ 2017-06-01 17:21:43 ] INFO Normalization arguments: [ 2017-06-01 17:21:43 ] INFO locfunc: [ 2017-06-01 17:21:43 ] INFO [[ [ 2017-06-01 17:21:43 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 17:21:43 ] INFO locfunc [ 2017-06-01 17:21:43 ] INFO Statistical algorithm: deseq [ 2017-06-01 17:21:43 ] INFO Statistical arguments: [ 2017-06-01 17:21:43 ] INFO deseq: blind, fit-only, local [ 2017-06-01 17:21:43 ] INFO Meta-analysis method: none [ 2017-06-01 17:21:43 ] INFO Multiple testing correction: BH [ 2017-06-01 17:21:43 ] INFO p-value threshold: 0.05 [ 2017-06-01 17:21:43 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 17:21:43 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 17:21:43 ] INFO Figure format: png, pdf [ 2017-06-01 17:21:43 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 17:21:43 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 17:21:43 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 17:21:43 ] INFO Output values: normalized [ 2017-06-01 17:21:43 ] INFO Downloading gene annotation for dm3... [ 2017-06-01 17:21:51 ] INFO Downloading transcript annotation for dm3... [ 2017-06-01 17:22:11 ] INFO Converting annotation to GenomicRanges object... [ 2017-06-01 17:22:11 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-06-01 17:35:18 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"... [ 2017-06-01 17:35:18 ] INFO 2017-06-01 17:35:18: Data processing started... [ 2017-06-01 17:35:18 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 17:35:18 ] INFO Conditions: Byn, Ras [ 2017-06-01 17:35:18 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 17:35:18 ] INFO Samples to exclude: none [ 2017-06-01 17:35:18 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 17:35:18 ] INFO Annotation: download [ 2017-06-01 17:35:18 ] INFO Organism: dm6 [ 2017-06-01 17:35:18 ] INFO Reference source: ensembl [ 2017-06-01 17:35:18 ] INFO Count type: utr [ 2017-06-01 17:35:18 ] INFO Exon filters: none applied [ 2017-06-01 17:35:18 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 17:35:18 ] INFO length: [ 2017-06-01 17:35:18 ] INFO length: 500 [ 2017-06-01 17:35:18 ] INFO avg.reads: [ 2017-06-01 17:35:18 ] INFO average.per.bp: 100 [ 2017-06-01 17:35:18 ] INFO quantile: 0.25 [ 2017-06-01 17:35:18 ] INFO expression: [ 2017-06-01 17:35:18 ] INFO median: TRUE [ 2017-06-01 17:35:18 ] INFO mean: FALSE [ 2017-06-01 17:35:18 ] INFO quantile: NA [ 2017-06-01 17:35:18 ] INFO known: NA [ 2017-06-01 17:35:18 ] INFO custom: NA [ 2017-06-01 17:35:18 ] INFO biotype: [ 2017-06-01 17:35:18 ] INFO pseudogene: FALSE [ 2017-06-01 17:35:18 ] INFO lincRNA: FALSE [ 2017-06-01 17:35:18 ] INFO protein_coding: FALSE [ 2017-06-01 17:35:18 ] INFO antisense: FALSE [ 2017-06-01 17:35:18 ] INFO processed_transcript: FALSE [ 2017-06-01 17:35:18 ] INFO snRNA: FALSE [ 2017-06-01 17:35:18 ] INFO sense_intronic: FALSE [ 2017-06-01 17:35:18 ] INFO miRNA: FALSE [ 2017-06-01 17:35:18 ] INFO misc_RNA: FALSE [ 2017-06-01 17:35:18 ] INFO snoRNA: FALSE [ 2017-06-01 17:35:18 ] INFO rRNA: TRUE [ 2017-06-01 17:35:18 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 17:35:18 ] INFO sense_overlapping: FALSE [ 2017-06-01 17:35:18 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 17:35:18 ] INFO TR_V_gene: FALSE [ 2017-06-01 17:35:18 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 17:35:18 ] INFO TR_D_gene: FALSE [ 2017-06-01 17:35:18 ] INFO TR_J_gene: FALSE [ 2017-06-01 17:35:18 ] INFO TR_C_gene: FALSE [ 2017-06-01 17:35:18 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 17:35:18 ] INFO IG_C_gene: FALSE [ 2017-06-01 17:35:18 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 17:35:18 ] INFO IG_J_gene: FALSE [ 2017-06-01 17:35:18 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 17:35:18 ] INFO IG_D_gene: FALSE [ 2017-06-01 17:35:18 ] INFO IG_V_gene: FALSE [ 2017-06-01 17:35:18 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 17:35:18 ] INFO Filter application: postnorm [ 2017-06-01 17:35:18 ] INFO Normalization algorithm: deseq [ 2017-06-01 17:35:18 ] INFO Normalization arguments: [ 2017-06-01 17:35:18 ] INFO locfunc: [ 2017-06-01 17:35:18 ] INFO [[ [ 2017-06-01 17:35:18 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 17:35:18 ] INFO locfunc [ 2017-06-01 17:35:18 ] INFO Statistical algorithm: deseq [ 2017-06-01 17:35:18 ] INFO Statistical arguments: [ 2017-06-01 17:35:18 ] INFO deseq: blind, fit-only, local [ 2017-06-01 17:35:18 ] INFO Meta-analysis method: none [ 2017-06-01 17:35:18 ] INFO Multiple testing correction: BH [ 2017-06-01 17:35:18 ] INFO p-value threshold: 0.05 [ 2017-06-01 17:35:18 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 17:35:18 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 17:35:18 ] INFO Figure format: png, pdf [ 2017-06-01 17:35:18 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 17:35:18 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 17:35:18 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 17:35:18 ] INFO Output values: normalized [ 2017-06-01 17:35:18 ] INFO Downloading gene annotation for dm6... [ 2017-06-01 17:35:26 ] INFO Downloading transcript annotation for dm6... [ 2017-06-01 17:36:01 ] INFO Converting annotation to GenomicRanges object... [ 2017-06-01 17:36:01 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-06-01 17:38:50 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"... [ 2017-06-01 17:38:50 ] INFO 2017-06-01 17:38:50: Data processing started... [ 2017-06-01 17:38:50 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 17:38:50 ] INFO Conditions: Byn, Ras [ 2017-06-01 17:38:50 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 17:38:50 ] INFO Samples to exclude: none [ 2017-06-01 17:38:50 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 17:38:50 ] INFO Annotation: download [ 2017-06-01 17:38:50 ] INFO Organism: dm3 [ 2017-06-01 17:38:50 ] INFO Reference source: ensembl [ 2017-06-01 17:38:50 ] INFO Count type: utr [ 2017-06-01 17:38:50 ] INFO Exon filters: none applied [ 2017-06-01 17:38:50 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 17:38:50 ] INFO length: [ 2017-06-01 17:38:50 ] INFO length: 500 [ 2017-06-01 17:38:50 ] INFO avg.reads: [ 2017-06-01 17:38:50 ] INFO average.per.bp: 100 [ 2017-06-01 17:38:50 ] INFO quantile: 0.25 [ 2017-06-01 17:38:50 ] INFO expression: [ 2017-06-01 17:38:50 ] INFO median: TRUE [ 2017-06-01 17:38:50 ] INFO mean: FALSE [ 2017-06-01 17:38:50 ] INFO quantile: NA [ 2017-06-01 17:38:50 ] INFO known: NA [ 2017-06-01 17:38:50 ] INFO custom: NA [ 2017-06-01 17:38:50 ] INFO biotype: [ 2017-06-01 17:38:50 ] INFO pseudogene: FALSE [ 2017-06-01 17:38:50 ] INFO lincRNA: FALSE [ 2017-06-01 17:38:50 ] INFO protein_coding: FALSE [ 2017-06-01 17:38:50 ] INFO antisense: FALSE [ 2017-06-01 17:38:50 ] INFO processed_transcript: FALSE [ 2017-06-01 17:38:50 ] INFO snRNA: FALSE [ 2017-06-01 17:38:50 ] INFO sense_intronic: FALSE [ 2017-06-01 17:38:50 ] INFO miRNA: FALSE [ 2017-06-01 17:38:50 ] INFO misc_RNA: FALSE [ 2017-06-01 17:38:50 ] INFO snoRNA: FALSE [ 2017-06-01 17:38:50 ] INFO rRNA: TRUE [ 2017-06-01 17:38:50 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 17:38:50 ] INFO sense_overlapping: FALSE [ 2017-06-01 17:38:50 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 17:38:50 ] INFO TR_V_gene: FALSE [ 2017-06-01 17:38:50 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 17:38:50 ] INFO TR_D_gene: FALSE [ 2017-06-01 17:38:50 ] INFO TR_J_gene: FALSE [ 2017-06-01 17:38:50 ] INFO TR_C_gene: FALSE [ 2017-06-01 17:38:50 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 17:38:50 ] INFO IG_C_gene: FALSE [ 2017-06-01 17:38:50 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 17:38:50 ] INFO IG_J_gene: FALSE [ 2017-06-01 17:38:50 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 17:38:50 ] INFO IG_D_gene: FALSE [ 2017-06-01 17:38:50 ] INFO IG_V_gene: FALSE [ 2017-06-01 17:38:50 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 17:38:50 ] INFO Filter application: postnorm [ 2017-06-01 17:38:50 ] INFO Normalization algorithm: deseq [ 2017-06-01 17:38:50 ] INFO Normalization arguments: [ 2017-06-01 17:38:50 ] INFO locfunc: [ 2017-06-01 17:38:50 ] INFO [[ [ 2017-06-01 17:38:50 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 17:38:50 ] INFO locfunc [ 2017-06-01 17:38:50 ] INFO Statistical algorithm: deseq [ 2017-06-01 17:38:50 ] INFO Statistical arguments: [ 2017-06-01 17:38:50 ] INFO deseq: blind, fit-only, local [ 2017-06-01 17:38:50 ] INFO Meta-analysis method: none [ 2017-06-01 17:38:50 ] INFO Multiple testing correction: BH [ 2017-06-01 17:38:50 ] INFO p-value threshold: 0.05 [ 2017-06-01 17:38:50 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 17:38:50 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 17:38:50 ] INFO Figure format: png, pdf [ 2017-06-01 17:38:50 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 17:38:50 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 17:38:50 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 17:38:50 ] INFO Output values: normalized [ 2017-06-01 17:38:50 ] INFO Downloading gene annotation for dm3... [ 2017-06-01 17:39:04 ] INFO Downloading transcript annotation for dm3... [ 2017-06-01 17:39:20 ] INFO Converting annotation to GenomicRanges object... [ 2017-06-01 17:39:20 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-06-01 17:50:03 ] FATAL "org" parameter must be one of "hg18", "hg19", "hg38", "mm9", "mm10", "rn5", "dm3", "danrer7", "pantro4", "susscr3", "tair10", "custom"! [ 2017-06-01 17:51:02 ] FATAL "org" parameter must be one of "hg18", "hg19", "hg38", "mm9", "mm10", "rn5", "dm3", "danrer7", "pantro4", "susscr3", "tair10", "custom"! [ 2017-06-01 17:52:54 ] INFO 2017-06-01 17:52:54: Data processing started... [ 2017-06-01 17:52:54 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 17:52:54 ] INFO Conditions: Byn, Ras [ 2017-06-01 17:52:54 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 17:52:54 ] INFO Samples to exclude: none [ 2017-06-01 17:52:54 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 17:52:54 ] INFO Annotation: download [ 2017-06-01 17:52:54 ] INFO Organism: dm6 [ 2017-06-01 17:52:54 ] INFO Reference source: ensembl [ 2017-06-01 17:52:54 ] INFO Count type: utr [ 2017-06-01 17:52:54 ] INFO Exon filters: none applied [ 2017-06-01 17:52:54 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 17:52:54 ] INFO length: [ 2017-06-01 17:52:54 ] INFO length: 500 [ 2017-06-01 17:52:54 ] INFO avg.reads: [ 2017-06-01 17:52:54 ] INFO average.per.bp: 100 [ 2017-06-01 17:52:54 ] INFO quantile: 0.25 [ 2017-06-01 17:52:54 ] INFO expression: [ 2017-06-01 17:52:54 ] INFO median: TRUE [ 2017-06-01 17:52:54 ] INFO mean: FALSE [ 2017-06-01 17:52:54 ] INFO quantile: NA [ 2017-06-01 17:52:54 ] INFO known: NA [ 2017-06-01 17:52:54 ] INFO custom: NA [ 2017-06-01 17:52:54 ] INFO biotype: [ 2017-06-01 17:52:54 ] INFO pseudogene: FALSE [ 2017-06-01 17:52:54 ] INFO lincRNA: FALSE [ 2017-06-01 17:52:54 ] INFO protein_coding: FALSE [ 2017-06-01 17:52:54 ] INFO antisense: FALSE [ 2017-06-01 17:52:54 ] INFO processed_transcript: FALSE [ 2017-06-01 17:52:54 ] INFO snRNA: FALSE [ 2017-06-01 17:52:54 ] INFO sense_intronic: FALSE [ 2017-06-01 17:52:54 ] INFO miRNA: FALSE [ 2017-06-01 17:52:54 ] INFO misc_RNA: FALSE [ 2017-06-01 17:52:54 ] INFO snoRNA: FALSE [ 2017-06-01 17:52:54 ] INFO rRNA: TRUE [ 2017-06-01 17:52:54 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 17:52:54 ] INFO sense_overlapping: FALSE [ 2017-06-01 17:52:54 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 17:52:54 ] INFO TR_V_gene: FALSE [ 2017-06-01 17:52:54 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 17:52:54 ] INFO TR_D_gene: FALSE [ 2017-06-01 17:52:54 ] INFO TR_J_gene: FALSE [ 2017-06-01 17:52:54 ] INFO TR_C_gene: FALSE [ 2017-06-01 17:52:54 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 17:52:54 ] INFO IG_C_gene: FALSE [ 2017-06-01 17:52:54 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 17:52:54 ] INFO IG_J_gene: FALSE [ 2017-06-01 17:52:54 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 17:52:54 ] INFO IG_D_gene: FALSE [ 2017-06-01 17:52:54 ] INFO IG_V_gene: FALSE [ 2017-06-01 17:52:54 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 17:52:54 ] INFO Filter application: postnorm [ 2017-06-01 17:52:54 ] INFO Normalization algorithm: deseq [ 2017-06-01 17:52:54 ] INFO Normalization arguments: [ 2017-06-01 17:52:54 ] INFO locfunc: [ 2017-06-01 17:52:54 ] INFO [[ [ 2017-06-01 17:52:54 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 17:52:54 ] INFO locfunc [ 2017-06-01 17:52:54 ] INFO Statistical algorithm: deseq [ 2017-06-01 17:52:54 ] INFO Statistical arguments: [ 2017-06-01 17:52:54 ] INFO deseq: blind, fit-only, local [ 2017-06-01 17:52:54 ] INFO Meta-analysis method: none [ 2017-06-01 17:52:54 ] INFO Multiple testing correction: BH [ 2017-06-01 17:52:54 ] INFO p-value threshold: 0.05 [ 2017-06-01 17:52:54 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 17:52:54 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 17:52:54 ] INFO Figure format: png, pdf [ 2017-06-01 17:52:54 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 17:52:54 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 17:52:54 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 17:52:54 ] INFO Output values: normalized [ 2017-06-01 17:52:54 ] INFO Downloading gene annotation for dm6... [ 2017-06-01 17:53:56 ] INFO 2017-06-01 17:53:56: Data processing started... [ 2017-06-01 17:53:56 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 17:53:56 ] INFO Conditions: Byn, Ras [ 2017-06-01 17:53:56 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 17:53:56 ] INFO Samples to exclude: none [ 2017-06-01 17:53:56 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 17:53:56 ] INFO Annotation: download [ 2017-06-01 17:53:56 ] INFO Organism: dm6 [ 2017-06-01 17:53:56 ] INFO Reference source: ensembl [ 2017-06-01 17:53:56 ] INFO Count type: utr [ 2017-06-01 17:53:56 ] INFO Exon filters: none applied [ 2017-06-01 17:53:56 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 17:53:56 ] INFO length: [ 2017-06-01 17:53:56 ] INFO length: 500 [ 2017-06-01 17:53:56 ] INFO avg.reads: [ 2017-06-01 17:53:56 ] INFO average.per.bp: 100 [ 2017-06-01 17:53:56 ] INFO quantile: 0.25 [ 2017-06-01 17:53:56 ] INFO expression: [ 2017-06-01 17:53:56 ] INFO median: TRUE [ 2017-06-01 17:53:56 ] INFO mean: FALSE [ 2017-06-01 17:53:56 ] INFO quantile: NA [ 2017-06-01 17:53:56 ] INFO known: NA [ 2017-06-01 17:53:56 ] INFO custom: NA [ 2017-06-01 17:53:56 ] INFO biotype: [ 2017-06-01 17:53:56 ] INFO pseudogene: FALSE [ 2017-06-01 17:53:56 ] INFO lincRNA: FALSE [ 2017-06-01 17:53:56 ] INFO protein_coding: FALSE [ 2017-06-01 17:53:56 ] INFO antisense: FALSE [ 2017-06-01 17:53:56 ] INFO processed_transcript: FALSE [ 2017-06-01 17:53:56 ] INFO snRNA: FALSE [ 2017-06-01 17:53:56 ] INFO sense_intronic: FALSE [ 2017-06-01 17:53:56 ] INFO miRNA: FALSE [ 2017-06-01 17:53:56 ] INFO misc_RNA: FALSE [ 2017-06-01 17:53:56 ] INFO snoRNA: FALSE [ 2017-06-01 17:53:56 ] INFO rRNA: TRUE [ 2017-06-01 17:53:56 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 17:53:56 ] INFO sense_overlapping: FALSE [ 2017-06-01 17:53:56 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 17:53:56 ] INFO TR_V_gene: FALSE [ 2017-06-01 17:53:56 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 17:53:56 ] INFO TR_D_gene: FALSE [ 2017-06-01 17:53:56 ] INFO TR_J_gene: FALSE [ 2017-06-01 17:53:56 ] INFO TR_C_gene: FALSE [ 2017-06-01 17:53:56 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 17:53:56 ] INFO IG_C_gene: FALSE [ 2017-06-01 17:53:56 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 17:53:56 ] INFO IG_J_gene: FALSE [ 2017-06-01 17:53:56 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 17:53:56 ] INFO IG_D_gene: FALSE [ 2017-06-01 17:53:56 ] INFO IG_V_gene: FALSE [ 2017-06-01 17:53:56 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 17:53:56 ] INFO Filter application: postnorm [ 2017-06-01 17:53:56 ] INFO Normalization algorithm: deseq [ 2017-06-01 17:53:56 ] INFO Normalization arguments: [ 2017-06-01 17:53:56 ] INFO locfunc: [ 2017-06-01 17:53:56 ] INFO [[ [ 2017-06-01 17:53:56 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 17:53:56 ] INFO locfunc [ 2017-06-01 17:53:56 ] INFO Statistical algorithm: deseq [ 2017-06-01 17:53:56 ] INFO Statistical arguments: [ 2017-06-01 17:53:56 ] INFO deseq: blind, fit-only, local [ 2017-06-01 17:53:56 ] INFO Meta-analysis method: none [ 2017-06-01 17:53:56 ] INFO Multiple testing correction: BH [ 2017-06-01 17:53:56 ] INFO p-value threshold: 0.05 [ 2017-06-01 17:53:56 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 17:53:56 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 17:53:56 ] INFO Figure format: png, pdf [ 2017-06-01 17:53:56 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 17:53:56 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 17:53:56 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 17:53:56 ] INFO Output values: normalized [ 2017-06-01 17:53:56 ] INFO Downloading gene annotation for dm6... [ 2017-06-01 18:24:58 ] INFO 2017-06-01 18:24:58: Data processing started... [ 2017-06-01 18:24:58 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 18:24:58 ] INFO Conditions: Byn, Ras [ 2017-06-01 18:24:58 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 18:24:58 ] INFO Samples to exclude: none [ 2017-06-01 18:24:58 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 18:24:58 ] INFO Annotation: download [ 2017-06-01 18:24:58 ] INFO Organism: dm6 [ 2017-06-01 18:24:58 ] INFO Reference source: ensembl [ 2017-06-01 18:24:58 ] INFO Count type: utr [ 2017-06-01 18:24:58 ] INFO Exon filters: none applied [ 2017-06-01 18:24:58 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 18:24:58 ] INFO length: [ 2017-06-01 18:24:58 ] INFO length: 500 [ 2017-06-01 18:24:58 ] INFO avg.reads: [ 2017-06-01 18:24:58 ] INFO average.per.bp: 100 [ 2017-06-01 18:24:58 ] INFO quantile: 0.25 [ 2017-06-01 18:24:58 ] INFO expression: [ 2017-06-01 18:24:58 ] INFO median: TRUE [ 2017-06-01 18:24:58 ] INFO mean: FALSE [ 2017-06-01 18:24:58 ] INFO quantile: NA [ 2017-06-01 18:24:58 ] INFO known: NA [ 2017-06-01 18:24:58 ] INFO custom: NA [ 2017-06-01 18:24:58 ] INFO biotype: [ 2017-06-01 18:24:58 ] INFO pseudogene: FALSE [ 2017-06-01 18:24:58 ] INFO lincRNA: FALSE [ 2017-06-01 18:24:58 ] INFO protein_coding: FALSE [ 2017-06-01 18:24:58 ] INFO antisense: FALSE [ 2017-06-01 18:24:58 ] INFO processed_transcript: FALSE [ 2017-06-01 18:24:58 ] INFO snRNA: FALSE [ 2017-06-01 18:24:58 ] INFO sense_intronic: FALSE [ 2017-06-01 18:24:58 ] INFO miRNA: FALSE [ 2017-06-01 18:24:58 ] INFO misc_RNA: FALSE [ 2017-06-01 18:24:58 ] INFO snoRNA: FALSE [ 2017-06-01 18:24:58 ] INFO rRNA: TRUE [ 2017-06-01 18:24:58 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 18:24:58 ] INFO sense_overlapping: FALSE [ 2017-06-01 18:24:58 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 18:24:58 ] INFO TR_V_gene: FALSE [ 2017-06-01 18:24:58 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 18:24:58 ] INFO TR_D_gene: FALSE [ 2017-06-01 18:24:58 ] INFO TR_J_gene: FALSE [ 2017-06-01 18:24:58 ] INFO TR_C_gene: FALSE [ 2017-06-01 18:24:58 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 18:24:58 ] INFO IG_C_gene: FALSE [ 2017-06-01 18:24:58 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 18:24:58 ] INFO IG_J_gene: FALSE [ 2017-06-01 18:24:58 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 18:24:58 ] INFO IG_D_gene: FALSE [ 2017-06-01 18:24:58 ] INFO IG_V_gene: FALSE [ 2017-06-01 18:24:58 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 18:24:58 ] INFO Filter application: postnorm [ 2017-06-01 18:24:58 ] INFO Normalization algorithm: deseq [ 2017-06-01 18:24:58 ] INFO Normalization arguments: [ 2017-06-01 18:24:58 ] INFO locfunc: [ 2017-06-01 18:24:58 ] INFO [[ [ 2017-06-01 18:24:58 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 18:24:58 ] INFO locfunc [ 2017-06-01 18:24:58 ] INFO Statistical algorithm: deseq [ 2017-06-01 18:24:58 ] INFO Statistical arguments: [ 2017-06-01 18:24:58 ] INFO deseq: blind, fit-only, local [ 2017-06-01 18:24:58 ] INFO Meta-analysis method: none [ 2017-06-01 18:24:58 ] INFO Multiple testing correction: BH [ 2017-06-01 18:24:58 ] INFO p-value threshold: 0.05 [ 2017-06-01 18:24:58 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 18:24:58 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 18:24:58 ] INFO Figure format: png, pdf [ 2017-06-01 18:24:58 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 18:24:58 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 18:24:58 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 18:24:58 ] INFO Output values: normalized [ 2017-06-01 18:24:58 ] INFO Downloading gene annotation for dm6... [ 2017-06-01 18:25:06 ] INFO Downloading transcript annotation for dm6... [ 2017-06-01 18:25:45 ] INFO Converting annotation to GenomicRanges object... [ 2017-06-01 18:25:45 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-06-01 18:26:37 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2017-06-01 18:26:38 ] INFO Reading bam file YA3R1-Byn1.bam for sample with name YA3R1-Byn1. This might take some time... [ 2017-06-01 18:26:38 ] INFO Reading bam file YA3R2-Byn2.bam for sample with name YA3R2-Byn2. This might take some time... [ 2017-06-01 18:26:38 ] INFO Reading bam file YA3R3-Byn3.bam for sample with name YA3R3-Byn3. This might take some time... [ 2017-06-01 18:26:38 ] INFO Reading bam file YA3R4-BynRas1.bam for sample with name YA3R4-BynRas1. This might take some time... [ 2017-06-01 18:26:38 ] INFO Reading bam file YA3R5-BynRas2.bam for sample with name YA3R5-BynRas2. This might take some time... [ 2017-06-01 18:26:38 ] INFO Reading bam file YA3R6-BynRas3.bam for sample with name YA3R6-BynRas3. This might take some time... [ 2017-06-01 18:26:40 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:26:40 ] INFO ...for single-end reads... [ 2017-06-01 18:26:40 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:26:41 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:26:41 ] INFO ...for single-end reads... [ 2017-06-01 18:26:41 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:26:42 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:26:42 ] INFO ...for single-end reads... [ 2017-06-01 18:26:42 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:26:42 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:26:42 ] INFO ...for single-end reads... [ 2017-06-01 18:26:42 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:26:43 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:26:43 ] INFO ...for single-end reads... [ 2017-06-01 18:26:43 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:26:43 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:26:43 ] INFO ...for single-end reads... [ 2017-06-01 18:26:43 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:27:10 ] INFO Exporting raw read counts table to /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347/lists/raw_counts_table.txt.gz [ 2017-06-01 18:27:11 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2017-06-01 18:27:11 ] INFO Processing transcripts... [ 2017-06-01 18:27:11 ] INFO Separating transcripts (UTR regions) per gene for YA3R1-Byn1... [ 2017-06-01 18:27:13 ] INFO Separating transcripts (UTR regions) per gene for YA3R2-Byn2... [ 2017-06-01 18:27:16 ] INFO Separating transcripts (UTR regions) per gene for YA3R3-Byn3... [ 2017-06-01 18:27:20 ] INFO Separating transcripts (UTR regions) per gene for YA3R4-BynRas1... [ 2017-06-01 18:27:24 ] INFO Separating transcripts (UTR regions) per gene for YA3R5-BynRas2... [ 2017-06-01 18:27:27 ] INFO Separating transcripts (UTR regions) per gene for YA3R6-BynRas3... [ 2017-06-01 18:27:31 ] INFO Saving gene model to /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347/data/gene_model.RData [ 2017-06-01 18:27:31 ] INFO Summarizing count data... [ 2017-06-01 18:27:37 ] INFO Removing genes with zero counts in all samples... [ 2017-06-01 18:27:37 ] INFO Normalizing with: deseq [ 2017-06-01 18:31:38 ] INFO 2017-06-01 18:31:38: Data processing started... [ 2017-06-01 18:31:38 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 18:31:38 ] INFO Conditions: Byn, Ras [ 2017-06-01 18:31:38 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 18:31:38 ] INFO Samples to exclude: none [ 2017-06-01 18:31:38 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 18:31:38 ] INFO Annotation: download [ 2017-06-01 18:31:38 ] INFO Organism: dm6 [ 2017-06-01 18:31:38 ] INFO Reference source: ensembl [ 2017-06-01 18:31:38 ] INFO Count type: utr [ 2017-06-01 18:31:38 ] INFO Exon filters: none applied [ 2017-06-01 18:31:38 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 18:31:38 ] INFO length: [ 2017-06-01 18:31:38 ] INFO length: 500 [ 2017-06-01 18:31:38 ] INFO avg.reads: [ 2017-06-01 18:31:38 ] INFO average.per.bp: 100 [ 2017-06-01 18:31:38 ] INFO quantile: 0.25 [ 2017-06-01 18:31:38 ] INFO expression: [ 2017-06-01 18:31:38 ] INFO median: TRUE [ 2017-06-01 18:31:38 ] INFO mean: FALSE [ 2017-06-01 18:31:38 ] INFO quantile: NA [ 2017-06-01 18:31:38 ] INFO known: NA [ 2017-06-01 18:31:38 ] INFO custom: NA [ 2017-06-01 18:31:38 ] INFO biotype: [ 2017-06-01 18:31:38 ] INFO pseudogene: FALSE [ 2017-06-01 18:31:38 ] INFO lincRNA: FALSE [ 2017-06-01 18:31:38 ] INFO protein_coding: FALSE [ 2017-06-01 18:31:38 ] INFO antisense: FALSE [ 2017-06-01 18:31:38 ] INFO processed_transcript: FALSE [ 2017-06-01 18:31:38 ] INFO snRNA: FALSE [ 2017-06-01 18:31:38 ] INFO sense_intronic: FALSE [ 2017-06-01 18:31:38 ] INFO miRNA: FALSE [ 2017-06-01 18:31:38 ] INFO misc_RNA: FALSE [ 2017-06-01 18:31:39 ] INFO snoRNA: FALSE [ 2017-06-01 18:31:39 ] INFO rRNA: TRUE [ 2017-06-01 18:31:39 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 18:31:39 ] INFO sense_overlapping: FALSE [ 2017-06-01 18:31:39 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 18:31:39 ] INFO TR_V_gene: FALSE [ 2017-06-01 18:31:39 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 18:31:39 ] INFO TR_D_gene: FALSE [ 2017-06-01 18:31:39 ] INFO TR_J_gene: FALSE [ 2017-06-01 18:31:39 ] INFO TR_C_gene: FALSE [ 2017-06-01 18:31:39 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 18:31:39 ] INFO IG_C_gene: FALSE [ 2017-06-01 18:31:39 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 18:31:39 ] INFO IG_J_gene: FALSE [ 2017-06-01 18:31:39 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 18:31:39 ] INFO IG_D_gene: FALSE [ 2017-06-01 18:31:39 ] INFO IG_V_gene: FALSE [ 2017-06-01 18:31:39 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 18:31:39 ] INFO Filter application: postnorm [ 2017-06-01 18:31:39 ] INFO Normalization algorithm: edger [ 2017-06-01 18:31:39 ] INFO Normalization arguments: [ 2017-06-01 18:31:39 ] INFO method: TMM [ 2017-06-01 18:31:39 ] INFO logratioTrim: 0.3 [ 2017-06-01 18:31:39 ] INFO sumTrim: 0.05 [ 2017-06-01 18:31:39 ] INFO doWeighting: TRUE [ 2017-06-01 18:31:39 ] INFO Acutoff: -1e+10 [ 2017-06-01 18:31:39 ] INFO p: 0.75 [ 2017-06-01 18:31:39 ] INFO Statistical algorithm: edger [ 2017-06-01 18:31:39 ] INFO Statistical arguments: [ 2017-06-01 18:31:39 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) [ 2017-06-01 18:31:39 ] INFO Meta-analysis method: none [ 2017-06-01 18:31:39 ] INFO Multiple testing correction: BH [ 2017-06-01 18:31:39 ] INFO p-value threshold: 0.05 [ 2017-06-01 18:31:39 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 18:31:39 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 18:31:39 ] INFO Figure format: png, pdf [ 2017-06-01 18:31:39 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 18:31:39 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 18:31:39 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 18:31:39 ] INFO Output values: normalized [ 2017-06-01 18:31:39 ] INFO Downloading gene annotation for dm6... [ 2017-06-01 18:31:49 ] INFO Downloading transcript annotation for dm6... [ 2017-06-01 18:32:19 ] INFO Converting annotation to GenomicRanges object... [ 2017-06-01 18:32:19 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-06-01 18:33:16 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2017-06-01 18:33:16 ] INFO Reading bam file YA3R1-Byn1.bam for sample with name YA3R1-Byn1. This might take some time... [ 2017-06-01 18:33:16 ] INFO Reading bam file YA3R2-Byn2.bam for sample with name YA3R2-Byn2. This might take some time... [ 2017-06-01 18:33:16 ] INFO Reading bam file YA3R3-Byn3.bam for sample with name YA3R3-Byn3. This might take some time... [ 2017-06-01 18:33:16 ] INFO Reading bam file YA3R4-BynRas1.bam for sample with name YA3R4-BynRas1. This might take some time... [ 2017-06-01 18:33:16 ] INFO Reading bam file YA3R5-BynRas2.bam for sample with name YA3R5-BynRas2. This might take some time... [ 2017-06-01 18:33:16 ] INFO Reading bam file YA3R6-BynRas3.bam for sample with name YA3R6-BynRas3. This might take some time... [ 2017-06-01 18:33:19 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:33:19 ] INFO ...for single-end reads... [ 2017-06-01 18:33:19 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:33:19 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:33:19 ] INFO ...for single-end reads... [ 2017-06-01 18:33:19 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:33:20 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:33:20 ] INFO ...for single-end reads... [ 2017-06-01 18:33:20 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:33:21 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:33:21 ] INFO ...for single-end reads... [ 2017-06-01 18:33:21 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:33:21 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:33:21 ] INFO ...for single-end reads... [ 2017-06-01 18:33:21 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:33:22 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:33:22 ] INFO ...for single-end reads... [ 2017-06-01 18:33:22 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:33:47 ] INFO Exporting raw read counts table to /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347/lists/raw_counts_table.txt.gz [ 2017-06-01 18:33:47 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2017-06-01 18:33:47 ] INFO Processing transcripts... [ 2017-06-01 18:33:47 ] INFO Separating transcripts (UTR regions) per gene for YA3R1-Byn1... [ 2017-06-01 18:33:51 ] INFO Separating transcripts (UTR regions) per gene for YA3R2-Byn2... [ 2017-06-01 18:33:54 ] INFO Separating transcripts (UTR regions) per gene for YA3R3-Byn3... [ 2017-06-01 18:33:58 ] INFO Separating transcripts (UTR regions) per gene for YA3R4-BynRas1... [ 2017-06-01 18:34:02 ] INFO Separating transcripts (UTR regions) per gene for YA3R5-BynRas2... [ 2017-06-01 18:34:06 ] INFO Separating transcripts (UTR regions) per gene for YA3R6-BynRas3... [ 2017-06-01 18:34:10 ] INFO Saving gene model to /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347/data/gene_model.RData [ 2017-06-01 18:34:11 ] INFO Summarizing count data... [ 2017-06-01 18:34:16 ] INFO Removing genes with zero counts in all samples... [ 2017-06-01 18:34:16 ] INFO Normalizing with: edger [ 2017-06-01 18:34:16 ] INFO Applying gene filter length... [ 2017-06-01 18:34:16 ] INFO Threshold below which ignored: 500 [ 2017-06-01 18:34:16 ] INFO Applying gene filter avg.reads... [ 2017-06-01 18:34:16 ] INFO Threshold below which ignored: -Inf [ 2017-06-01 18:34:16 ] INFO Applying gene filter expression... [ 2017-06-01 18:34:16 ] INFO Threshold below which ignored: NA [ 2017-06-01 18:34:16 ] INFO Applying gene filter biotype... [ 2017-06-01 18:34:16 ] INFO Biotypes ignored: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene [ 2017-06-01 18:57:22 ] INFO 2017-06-01 18:57:22: Data processing started... [ 2017-06-01 18:57:22 ] INFO Read counts file: imported sam/bam/bed files [ 2017-06-01 18:57:22 ] INFO Conditions: Byn, Ras [ 2017-06-01 18:57:22 ] INFO Samples to include: YA3R1-Byn1, YA3R2-Byn2, YA3R3-Byn3, YA3R4-BynRas1, YA3R5-BynRas2, YA3R6-BynRas3 [ 2017-06-01 18:57:22 ] INFO Samples to exclude: none [ 2017-06-01 18:57:22 ] INFO Requested contrasts: Byn_vs_Ras [ 2017-06-01 18:57:22 ] INFO Annotation: download [ 2017-06-01 18:57:22 ] INFO Organism: dm6 [ 2017-06-01 18:57:22 ] INFO Reference source: ensembl [ 2017-06-01 18:57:22 ] INFO Count type: utr [ 2017-06-01 18:57:22 ] INFO Exon filters: none applied [ 2017-06-01 18:57:22 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-06-01 18:57:22 ] INFO length: [ 2017-06-01 18:57:22 ] INFO length: 500 [ 2017-06-01 18:57:22 ] INFO avg.reads: [ 2017-06-01 18:57:22 ] INFO average.per.bp: 100 [ 2017-06-01 18:57:22 ] INFO quantile: 0.25 [ 2017-06-01 18:57:22 ] INFO expression: [ 2017-06-01 18:57:22 ] INFO median: TRUE [ 2017-06-01 18:57:22 ] INFO mean: FALSE [ 2017-06-01 18:57:22 ] INFO quantile: NA [ 2017-06-01 18:57:22 ] INFO known: NA [ 2017-06-01 18:57:22 ] INFO custom: NA [ 2017-06-01 18:57:22 ] INFO biotype: [ 2017-06-01 18:57:22 ] INFO pseudogene: FALSE [ 2017-06-01 18:57:22 ] INFO lincRNA: FALSE [ 2017-06-01 18:57:22 ] INFO protein_coding: FALSE [ 2017-06-01 18:57:22 ] INFO antisense: FALSE [ 2017-06-01 18:57:22 ] INFO processed_transcript: FALSE [ 2017-06-01 18:57:22 ] INFO snRNA: FALSE [ 2017-06-01 18:57:22 ] INFO sense_intronic: FALSE [ 2017-06-01 18:57:22 ] INFO miRNA: FALSE [ 2017-06-01 18:57:22 ] INFO misc_RNA: FALSE [ 2017-06-01 18:57:22 ] INFO snoRNA: FALSE [ 2017-06-01 18:57:22 ] INFO rRNA: TRUE [ 2017-06-01 18:57:22 ] INFO polymorphic_pseudogene: FALSE [ 2017-06-01 18:57:22 ] INFO sense_overlapping: FALSE [ 2017-06-01 18:57:22 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-06-01 18:57:22 ] INFO TR_V_gene: FALSE [ 2017-06-01 18:57:22 ] INFO TR_V_pseudogene: TRUE [ 2017-06-01 18:57:22 ] INFO TR_D_gene: FALSE [ 2017-06-01 18:57:22 ] INFO TR_J_gene: FALSE [ 2017-06-01 18:57:22 ] INFO TR_C_gene: FALSE [ 2017-06-01 18:57:22 ] INFO TR_J_pseudogene: TRUE [ 2017-06-01 18:57:22 ] INFO IG_C_gene: FALSE [ 2017-06-01 18:57:22 ] INFO IG_C_pseudogene: TRUE [ 2017-06-01 18:57:22 ] INFO IG_J_gene: FALSE [ 2017-06-01 18:57:22 ] INFO IG_J_pseudogene: TRUE [ 2017-06-01 18:57:22 ] INFO IG_D_gene: FALSE [ 2017-06-01 18:57:22 ] INFO IG_V_gene: FALSE [ 2017-06-01 18:57:22 ] INFO IG_V_pseudogene: TRUE [ 2017-06-01 18:57:22 ] INFO Filter application: postnorm [ 2017-06-01 18:57:22 ] INFO Normalization algorithm: deseq [ 2017-06-01 18:57:22 ] INFO Normalization arguments: [ 2017-06-01 18:57:22 ] INFO locfunc: [ 2017-06-01 18:57:22 ] INFO [[ [ 2017-06-01 18:57:22 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-06-01 18:57:22 ] INFO locfunc [ 2017-06-01 18:57:22 ] INFO Statistical algorithm: deseq [ 2017-06-01 18:57:22 ] INFO Statistical arguments: [ 2017-06-01 18:57:22 ] INFO deseq: blind, fit-only, local [ 2017-06-01 18:57:22 ] INFO Meta-analysis method: none [ 2017-06-01 18:57:22 ] INFO Multiple testing correction: BH [ 2017-06-01 18:57:22 ] INFO p-value threshold: 0.05 [ 2017-06-01 18:57:22 ] INFO Logarithmic transformation offset: 1 [ 2017-06-01 18:57:22 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-06-01 18:57:22 ] INFO Figure format: png, pdf [ 2017-06-01 18:57:22 ] INFO Output directory: /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347 [ 2017-06-01 18:57:22 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-06-01 18:57:22 ] INFO Output scale(s): log2, rpgm [ 2017-06-01 18:57:22 ] INFO Output values: normalized [ 2017-06-01 18:57:22 ] INFO Downloading gene annotation for dm6... [ 2017-06-01 18:57:32 ] INFO Downloading transcript annotation for dm6... [ 2017-06-01 18:57:58 ] INFO Converting annotation to GenomicRanges object... [ 2017-06-01 18:57:58 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-06-01 18:58:56 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2017-06-01 18:58:57 ] INFO Reading bam file YA3R1-Byn1.bam.chr.bam for sample with name YA3R1-Byn1. This might take some time... [ 2017-06-01 18:58:57 ] INFO Reading bam file YA3R2-Byn2.bam.chr.bam for sample with name YA3R2-Byn2. This might take some time... [ 2017-06-01 18:58:57 ] INFO Reading bam file YA3R3-Byn3.bam.chr.bam for sample with name YA3R3-Byn3. This might take some time... [ 2017-06-01 18:58:57 ] INFO Reading bam file YA3R4-BynRas1.bam.chr.bam for sample with name YA3R4-BynRas1. This might take some time... [ 2017-06-01 18:58:57 ] INFO Reading bam file YA3R5-BynRas2.bam.chr.bam for sample with name YA3R5-BynRas2. This might take some time... [ 2017-06-01 18:58:57 ] INFO Reading bam file YA3R6-BynRas3.bam.chr.bam for sample with name YA3R6-BynRas3. This might take some time... [ 2017-06-01 18:58:59 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:58:59 ] INFO ...for single-end reads... [ 2017-06-01 18:58:59 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:58:59 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:58:59 ] INFO ...for single-end reads... [ 2017-06-01 18:58:59 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:59:00 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:59:00 ] INFO ...for single-end reads... [ 2017-06-01 18:59:00 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:59:01 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:59:01 ] INFO ...for single-end reads... [ 2017-06-01 18:59:01 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:59:02 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:59:02 ] INFO ...for single-end reads... [ 2017-06-01 18:59:02 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:59:02 ] INFO Counting reads overlapping with given annotation... [ 2017-06-01 18:59:02 ] INFO ...for single-end reads... [ 2017-06-01 18:59:02 ] INFO ...assuming forward sequenced reads... [ 2017-06-01 18:59:27 ] INFO Exporting raw read counts table to /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347/lists/raw_counts_table.txt.gz [ 2017-06-01 18:59:27 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2017-06-01 18:59:27 ] INFO Processing transcripts... [ 2017-06-01 18:59:27 ] INFO Separating transcripts (UTR regions) per gene for YA3R1-Byn1... [ 2017-06-01 18:59:31 ] INFO Separating transcripts (UTR regions) per gene for YA3R2-Byn2... [ 2017-06-01 18:59:35 ] INFO Separating transcripts (UTR regions) per gene for YA3R3-Byn3... [ 2017-06-01 18:59:38 ] INFO Separating transcripts (UTR regions) per gene for YA3R4-BynRas1... [ 2017-06-01 18:59:42 ] INFO Separating transcripts (UTR regions) per gene for YA3R5-BynRas2... [ 2017-06-01 18:59:45 ] INFO Separating transcripts (UTR regions) per gene for YA3R6-BynRas3... [ 2017-06-01 18:59:49 ] INFO Saving gene model to /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347/data/gene_model.RData [ 2017-06-01 18:59:50 ] INFO Summarizing count data... [ 2017-06-01 18:59:54 ] INFO Removing genes with zero counts in all samples... [ 2017-06-01 18:59:54 ] INFO Normalizing with: deseq [ 2017-06-01 18:59:54 ] INFO Applying gene filter length... [ 2017-06-01 18:59:54 ] INFO Threshold below which ignored: 500 [ 2017-06-01 18:59:54 ] INFO Applying gene filter avg.reads... [ 2017-06-01 18:59:54 ] INFO Threshold below which ignored: 0.0777848124548635 [ 2017-06-01 18:59:54 ] INFO Applying gene filter expression... [ 2017-06-01 18:59:54 ] INFO Threshold below which ignored: 10 [ 2017-06-01 18:59:54 ] INFO Applying gene filter biotype... [ 2017-06-01 18:59:54 ] INFO Biotypes ignored: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene [ 2017-06-01 18:59:54 ] INFO 10309 genes filtered out [ 2017-06-01 18:59:54 ] INFO 7075 genes remain after filtering [ 2017-06-01 18:59:54 ] INFO Running statistical tests with: deseq [ 2017-06-01 18:59:54 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:00:00 ] INFO Contrast Byn_vs_Ras: found 1204 genes [ 2017-06-01 19:00:00 ] INFO Exporting and compressing normalized read counts table to /data/images/proton2/run347/wwwDrApidianakis/metaseqr_Apidianakis_run347/lists/normalized_counts_table.txt [ 2017-06-01 19:00:00 ] INFO Building output files... [ 2017-06-01 19:00:00 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:00:00 ] INFO Adding non-filtered data... [ 2017-06-01 19:00:00 ] INFO binding annotation... [ 2017-06-01 19:00:00 ] INFO binding p-values... [ 2017-06-01 19:00:00 ] INFO binding FDRs... [ 2017-06-01 19:00:01 ] INFO binding log2 normalized fold changes... [ 2017-06-01 19:00:01 ] INFO binding all normalized counts for Byn... [ 2017-06-01 19:00:01 ] INFO binding all normalized counts for Ras... [ 2017-06-01 19:00:01 ] INFO binding filtering flags... [ 2017-06-01 19:00:01 ] INFO Writing output... [ 2017-06-01 19:00:01 ] INFO Adding filtered data... [ 2017-06-01 19:00:01 ] INFO binding annotation... [ 2017-06-01 19:00:01 ] INFO binding p-values... [ 2017-06-01 19:00:01 ] INFO binding FDRs... [ 2017-06-01 19:00:02 ] INFO binding log2 normalized fold changes... [ 2017-06-01 19:00:02 ] INFO binding all normalized counts for Byn... [ 2017-06-01 19:00:02 ] INFO binding all normalized counts for Ras... [ 2017-06-01 19:00:02 ] INFO binding filtering flags... [ 2017-06-01 19:00:02 ] INFO Writing output... [ 2017-06-01 19:00:03 ] INFO Creating quality control graphs... [ 2017-06-01 19:00:03 ] INFO Plotting in png format... [ 2017-06-01 19:00:03 ] INFO Plotting mds... [ 2017-06-01 19:00:03 ] INFO Plotting biodetection... [ 2017-06-01 19:00:04 ] INFO Plotting countsbio... [ 2017-06-01 19:00:05 ] INFO Plotting saturation... [ 2017-06-01 19:00:08 ] INFO Plotting readnoise... [ 2017-06-01 19:00:09 ] INFO Plotting correl... [ 2017-06-01 19:00:09 ] INFO Plotting pairwise... [ 2017-06-01 19:00:14 ] INFO Plotting boxplot... [ 2017-06-01 19:00:14 ] INFO Plotting gcbias... [ 2017-06-01 19:00:14 ] INFO Plotting lengthbias... [ 2017-06-01 19:00:15 ] INFO Plotting meandiff... [ 2017-06-01 19:00:15 ] INFO Plotting meanvar... [ 2017-06-01 19:00:18 ] INFO Plotting boxplot... [ 2017-06-01 19:00:18 ] INFO Plotting gcbias... [ 2017-06-01 19:00:19 ] INFO Plotting lengthbias... [ 2017-06-01 19:00:19 ] INFO Plotting meandiff... [ 2017-06-01 19:00:20 ] INFO Plotting meanvar... [ 2017-06-01 19:00:22 ] INFO Plotting biodist... [ 2017-06-01 19:00:22 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:00:22 ] INFO Plotting volcano... [ 2017-06-01 19:00:22 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:00:23 ] INFO Plotting deheatmap... [ 2017-06-01 19:00:23 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:00:37 ] INFO Plotting filtered... [ 2017-06-01 19:00:37 ] INFO Plotting in pdf format... [ 2017-06-01 19:00:37 ] INFO Plotting mds... [ 2017-06-01 19:00:37 ] INFO Plotting biodetection... [ 2017-06-01 19:00:37 ] INFO Plotting countsbio... [ 2017-06-01 19:00:38 ] INFO Plotting saturation... [ 2017-06-01 19:00:39 ] INFO Plotting readnoise... [ 2017-06-01 19:00:40 ] INFO Plotting correl... [ 2017-06-01 19:00:40 ] INFO Plotting pairwise... [ 2017-06-01 19:00:42 ] INFO Plotting boxplot... [ 2017-06-01 19:00:42 ] INFO Plotting gcbias... [ 2017-06-01 19:00:43 ] INFO Plotting lengthbias... [ 2017-06-01 19:00:43 ] INFO Plotting meandiff... [ 2017-06-01 19:00:44 ] INFO Plotting meanvar... [ 2017-06-01 19:00:47 ] INFO Plotting boxplot... [ 2017-06-01 19:00:47 ] INFO Plotting gcbias... [ 2017-06-01 19:00:48 ] INFO Plotting lengthbias... [ 2017-06-01 19:00:48 ] INFO Plotting meandiff... [ 2017-06-01 19:00:49 ] INFO Plotting meanvar... [ 2017-06-01 19:00:52 ] INFO Plotting biodist... [ 2017-06-01 19:00:52 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:00:52 ] INFO Plotting volcano... [ 2017-06-01 19:00:52 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:00:52 ] INFO Plotting deheatmap... [ 2017-06-01 19:00:52 ] INFO Contrast: Byn_vs_Ras [ 2017-06-01 19:01:04 ] INFO Plotting filtered... [ 2017-06-01 19:01:05 ] INFO Creating HTML report... [ 2017-06-01 19:01:05 ] INFO Compressing figures...
Multidimensional scaling
Biotype detection
Biotype detection counts
Read and biotype saturation
RNA-Seq reads noise
Correlation plots
Pairwise scatterplots
Boxplots
GC content bias
Gene/transcript length bias
Mean-difference
Mean-variance
Chromosome and biotype distribution of filtered genes
Volcano plots
DEG heatmaps
Chromosome and biotype distributions of DEGs
Results
DEG table for the contrast Byn_vs_RasThe following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Byn_vs_Ras. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right. | chromosome | start | end | gene_id | gc_content | strand | gene_name | biotype | p-value_deseq | FDR_deseq | log2_normalized_fold_change_Byn_vs_Ras | log2_normalized_counts_YA3R1-Byn1 | log2_normalized_counts_YA3R2-Byn2 | log2_normalized_counts_YA3R3-Byn3 | rpgm_normalized_counts_YA3R1-Byn1 | rpgm_normalized_counts_YA3R2-Byn2 | rpgm_normalized_counts_YA3R3-Byn3 | log2_normalized_counts_YA3R4-BynRas1 | log2_normalized_counts_YA3R5-BynRas2 | log2_normalized_counts_YA3R6-BynRas3 | rpgm_normalized_counts_YA3R4-BynRas1 | rpgm_normalized_counts_YA3R5-BynRas2 | rpgm_normalized_counts_YA3R6-BynRas3 | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chrX | 17203112 | 17203925 | FBgn0030824 | 0.5467 | + | CG5070 | protein_coding | 5.07e-26 | 3.59e-22 | 7.36287 | 6.66e+00 | 7.31e+00 | 2.00e+00 | 9.09e-02 | 1.44e-01 | 2.73e-03 | 1.40e+01 | 1.38e+01 | 1.36e+01 | 1.49e+01 | 1.31e+01 | 1.16e+01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 17625268 | 17626086 | FBgn0038530 | 0.4762 | + | AttD | protein_coding | 6.91e-25 | 2.45e-21 | 7.79166 | 3.32e+00 | 2.81e+00 | 4.00e+00 | 6.36e-03 | 4.24e-03 | 1.06e-02 | 1.11e+01 | 1.15e+01 | 1.11e+01 | 1.54e+00 | 2.04e+00 | 1.58e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 16609220 | 16611325 | FBgn0027109 | 0.4231 | + | NPF | protein_coding | 1.63e-23 | 3.84e-20 | 8.35226 | 0.00e+00 | 1.00e+00 | 1.00e+00 | 0.00e+00 | 6.85e-04 | 6.85e-04 | 9.33e+00 | 8.81e+00 | 9.07e+00 | 4.41e-01 | 3.08e-01 | 3.68e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 11233192 | 11233714 | FBgn0033587 | 0.5315 | - | CG13218 | protein_coding | 6.06e-22 | 1.07e-18 | 7.85019 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 9.34e-04 | 8.83e+00 | 8.01e+00 | 7.71e+00 | 4.25e-01 | 2.40e-01 | 1.94e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 20354108 | 20355067 | FBgn0034507 | 0.5469 | - | CG11192 | protein_coding | 4.92e-20 | 6.96e-17 | 6.35513 | 6.29e+00 | 5.25e+00 | 4.46e+00 | 6.97e-02 | 3.35e-02 | 1.90e-02 | 1.19e+01 | 1.17e+01 | 1.20e+01 | 3.57e+00 | 3.06e+00 | 3.59e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 30243978 | 30246703 | FBgn0039759 | 0.4633 | - | CG9733 | protein_coding | 1.93e-19 | 2.27e-16 | 6.76155 | 0.00e+00 | 0.00e+00 | 2.00e+00 | 0.00e+00 | 0.00e+00 | 2.14e-03 | 7.85e+00 | 8.09e+00 | 7.20e+00 | 1.64e-01 | 1.94e-01 | 1.04e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 17413077 | 17413639 | FBgn0262003 | 0.4067 | + | CG42821 | protein_coding | 8.08e-19 | 8.16e-16 | 6.24271 | 4.32e+00 | 5.55e+00 | 5.52e+00 | 1.38e-02 | 3.35e-02 | 3.28e-02 | 1.16e+01 | 1.15e+01 | 1.13e+01 | 2.30e+00 | 2.08e+00 | 1.85e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 7413869 | 7414662 | FBgn0261616 | 0.3741 | + | CG42705 | protein_coding | 2.18e-18 | 1.92e-15 | -5.78136 | 7.24e+00 | 7.48e+00 | 5.78e+00 | 8.68e-02 | 1.03e-01 | 3.12e-02 | 0.00e+00 | 2.00e+00 | 1.00e+00 | 0.00e+00 | 1.74e-03 | 5.79e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 7412668 | 7413296 | FBgn0261615 | 0.3641 | + | CG42704 | protein_coding | 4.35e-18 | 3.42e-15 | -5.81669 | 8.67e+00 | 7.56e+00 | 4.58e+00 | 2.91e-01 | 1.35e-01 | 1.65e-02 | 0.00e+00 | 3.00e+00 | 1.00e+00 | 0.00e+00 | 5.01e-03 | 7.16e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 810577 | 811531 | FBgn0051658 | 0.4209 | + | Nnf1b | protein_coding | 3.80e-17 | 2.69e-14 | 5.98558 | 1.00e+00 | 1.58e+00 | 2.58e+00 | 7.28e-04 | 1.46e-03 | 3.64e-03 | 3.81e+00 | 4.58e+00 | 9.36e+00 | 9.46e-03 | 1.67e-02 | 4.79e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 17411108 | 17412680 | FBgn0038507 | 0.4806 | + | CG5863 | protein_coding | 9.93e-16 | 6.14e-13 | 5.83036 | 0.00e+00 | 3.70e+00 | 2.58e+00 | 0.00e+00 | 9.11e-03 | 3.80e-03 | 9.16e+00 | 8.30e+00 | 7.97e+00 | 4.34e-01 | 2.38e-01 | 1.90e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 2251510 | 2252341 | FBgn0042186 | 0.5180 | - | CG17239 | protein_coding | 1.04e-15 | 6.14e-13 | -5.72792 | 2.00e+00 | 6.00e+00 | 7.17e+00 | 2.80e-03 | 5.87e-02 | 1.33e-01 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 9.32e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 20964527 | 20965419 | FBgn0031141 | 0.5207 | - | CG1304 | protein_coding | 1.44e-15 | 7.82e-13 | 6.29155 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 7.03e+00 | 5.98e+00 | 5.36e+00 | 1.19e-01 | 5.67e-02 | 3.66e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 15825747 | 15830321 | FBgn0038366 | 0.4555 | + | CG4576 | protein_coding | 1.36e-14 | 6.89e-12 | 5.93074 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 7.54e-04 | 0.00e+00 | 0.00e+00 | 5.73e+00 | 6.38e+00 | 6.75e+00 | 3.92e-02 | 6.18e-02 | 8.06e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 13279721 | 13284527 | FBgn0038130 | 0.4516 | + | CG8630 | protein_coding | 1.39e-13 | 6.55e-11 | 4.99435 | 1.00e+00 | 2.58e+00 | 3.00e+00 | 5.41e-04 | 2.70e-03 | 3.79e-03 | 7.24e+00 | 7.07e+00 | 7.81e+00 | 8.11e-02 | 7.19e-02 | 1.21e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 9372931 | 9374964 | FBgn0001223 | 0.4322 | + | Hsp22 | protein_coding | 2.87e-13 | 1.27e-10 | 4.95420 | 2.81e+00 | 3.32e+00 | 1.00e+00 | 4.10e-03 | 6.15e-03 | 6.83e-04 | 7.47e+00 | 7.71e+00 | 7.66e+00 | 1.20e-01 | 1.43e-01 | 1.37e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 9372722 | 9374964 | FBgn0001228 | 0.4289 | + | Hsp67Bb | protein_coding | 3.59e-13 | 1.49e-10 | 4.93782 | 3.00e+00 | 3.32e+00 | 1.00e+00 | 2.50e-03 | 3.22e-03 | 3.58e-04 | 7.50e+00 | 7.82e+00 | 7.69e+00 | 6.44e-02 | 8.05e-02 | 7.33e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 14345915 | 14346688 | FBgn0264253 | 0.4729 | - | Send2 | protein_coding | 3.95e-13 | 1.55e-10 | -5.62449 | 0.00e+00 | 3.58e+00 | 7.08e+00 | 0.00e+00 | 1.08e-02 | 1.32e-01 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 1463811 | 1468944 | FBgn0004635 | 0.4221 | + | rho | protein_coding | 4.60e-13 | 1.71e-10 | 5.38082 | 0.00e+00 | 1.58e+00 | 1.00e+00 | 0.00e+00 | 6.98e-04 | 3.49e-04 | 6.63e+00 | 6.75e+00 | 5.43e+00 | 3.42e-02 | 3.73e-02 | 1.47e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 14749223 | 14750165 | FBgn0041581 | 0.4645 | + | AttB | protein_coding | 6.64e-13 | 2.35e-10 | 4.99305 | 1.00e+00 | 4.00e+00 | 3.00e+00 | 6.83e-04 | 1.02e-02 | 4.78e-03 | 7.50e+00 | 8.28e+00 | 8.40e+00 | 1.23e-01 | 2.11e-01 | 2.29e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 6415179 | 6423310 | FBgn0011722 | 0.5300 | - | Tig | protein_coding | 1.19e-12 | 3.99e-10 | 4.74855 | 5.39e+00 | 4.95e+00 | 4.32e+00 | 2.68e-02 | 1.96e-02 | 1.24e-02 | 1.00e+01 | 9.86e+00 | 9.08e+00 | 6.73e-01 | 6.05e-01 | 3.52e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 11561643 | 11562779 | FBgn0030310 | 0.5092 | + | PGRP-SA | protein_coding | 1.45e-12 | 4.67e-10 | 4.59991 | 3.81e+00 | 3.00e+00 | 2.58e+00 | 9.62e-03 | 5.18e-03 | 3.70e-03 | 8.01e+00 | 7.68e+00 | 7.76e+00 | 1.89e-01 | 1.51e-01 | 1.60e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 685942 | 687958 | FBgn0035154 | 0.4948 | - | CG3344 | protein_coding | 3.00e-12 | 9.23e-10 | 4.72489 | 2.81e+00 | 0.00e+00 | 0.00e+00 | 4.53e-03 | 0.00e+00 | 0.00e+00 | 6.51e+00 | 6.29e+00 | 6.11e+00 | 6.80e-02 | 5.82e-02 | 5.14e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 14747362 | 14748215 | FBgn0012042 | 0.4778 | + | AttA | protein_coding | 3.86e-12 | 1.11e-09 | 4.98706 | 1.00e+00 | 5.00e+00 | 0.00e+00 | 7.30e-04 | 2.26e-02 | 0.00e+00 | 7.38e+00 | 8.68e+00 | 9.06e+00 | 1.20e-01 | 2.98e-01 | 3.90e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 7466543 | 7472493 | FBgn0031918 | 0.4028 | + | CG6055 | protein_coding | 3.94e-12 | 1.11e-09 | 4.44167 | 3.00e+00 | 2.58e+00 | 3.58e+00 | 4.48e-03 | 3.20e-03 | 7.04e-03 | 7.73e+00 | 7.54e+00 | 7.38e+00 | 1.35e-01 | 1.18e-01 | 1.06e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 17767808 | 17769989 | FBgn0034279 | 0.5156 | - | CG18635 | protein_coding | 1.20e-11 | 3.26e-09 | 4.85300 | 1.00e+00 | 2.81e+00 | 0.00e+00 | 7.60e-04 | 4.56e-03 | 0.00e+00 | 6.34e+00 | 6.60e+00 | 6.79e+00 | 6.08e-02 | 7.30e-02 | 8.37e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 11161207 | 11163498 | FBgn0027584 | 0.4367 | + | CG4757 | protein_coding | 1.64e-11 | 4.30e-09 | 4.71187 | 1.00e+00 | 4.70e+00 | 0.00e+00 | 5.89e-04 | 1.47e-02 | 0.00e+00 | 8.04e+00 | 8.16e+00 | 7.71e+00 | 1.55e-01 | 1.68e-01 | 1.22e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 8145758 | 8158786 | FBgn0263256 | 0.4073 | + | CG43394 | protein_coding | 2.41e-11 | 6.08e-09 | 4.21229 | 7.52e+00 | 6.86e+00 | 6.81e+00 | 3.89e-02 | 2.45e-02 | 2.36e-02 | 1.10e+01 | 1.13e+01 | 1.16e+01 | 4.30e-01 | 5.19e-01 | 6.74e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 24970843 | 24973207 | FBgn0035089 | 0.4820 | - | Phk-3 | protein_coding | 2.69e-11 | 6.56e-09 | 4.24907 | 7.11e+00 | 7.18e+00 | 6.83e+00 | 9.99e-02 | 1.05e-01 | 8.24e-02 | 1.17e+01 | 1.11e+01 | 1.10e+01 | 2.41e+00 | 1.62e+00 | 1.47e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 10688734 | 10689271 | FBgn0032284 | 0.5688 | - | CG7294 | protein_coding | 3.25e-11 | 7.56e-09 | 4.24911 | 4.39e+00 | 3.58e+00 | 4.95e+00 | 1.86e-02 | 1.02e-02 | 2.78e-02 | 8.37e+00 | 8.49e+00 | 9.04e+00 | 3.05e-01 | 3.32e-01 | 4.89e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 10640286 | 10661013 | FBgn0052066 | 0.3836 | - | CG32066 | protein_coding | 3.31e-11 | 7.56e-09 | -4.48938 | 3.91e+00 | 3.00e+00 | 1.02e+01 | 6.39e-03 | 3.20e-03 | 5.22e-01 | 4.58e+00 | 4.52e+00 | 2.32e+00 | 1.05e-02 | 1.00e-02 | 1.83e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 11873319 | 11875346 | FBgn0030347 | 0.4714 | + | CG15739 | protein_coding | 5.46e-11 | 1.21e-08 | 4.23840 | 3.32e+00 | 2.32e+00 | 0.00e+00 | 5.31e-03 | 2.36e-03 | 0.00e+00 | 6.88e+00 | 6.29e+00 | 6.73e+00 | 6.90e-02 | 4.54e-02 | 6.19e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 10686124 | 10687066 | FBgn0032283 | 0.4995 | - | CG7296 | protein_coding | 6.86e-11 | 1.47e-08 | 3.71157 | 1.10e+01 | 1.04e+01 | 9.50e+00 | 1.55e+00 | 1.03e+00 | 5.41e-01 | 1.42e+01 | 1.40e+01 | 1.42e+01 | 1.43e+01 | 1.23e+01 | 1.43e+01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 22766732 | 22767699 | FBgn0040588 | 0.3936 | - | CG13841 | protein_coding | 7.24e-11 | 1.51e-08 | 5.42626 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 5.25e+00 | 5.55e+00 | 5.46e+00 | 2.16e-02 | 2.69e-02 | 2.51e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 17413901 | 17414607 | FBgn0262004 | 0.3975 | + | CG42822 | protein_coding | 1.67e-10 | 3.38e-08 | 4.65105 | 0.00e+00 | 2.32e+00 | 1.00e+00 | 0.00e+00 | 2.70e-03 | 6.74e-04 | 6.48e+00 | 5.95e+00 | 5.64e+00 | 5.93e-02 | 4.11e-02 | 3.30e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 12390166 | 12395980 | FBgn0038032 | 0.4335 | - | CG10096 | protein_coding | 2.33e-10 | 4.59e-08 | -3.97790 | 8.61e+00 | 8.60e+00 | 8.60e+00 | 1.94e-01 | 1.92e-01 | 1.92e-01 | 4.32e+00 | 4.91e+00 | 4.58e+00 | 9.43e-03 | 1.44e-02 | 1.14e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 12390166 | 12395980 | FBgn0038033 | 0.4335 | - | CG10097 | protein_coding | 2.57e-10 | 4.92e-08 | -4.01568 | 9.61e+00 | 9.58e+00 | 9.59e+00 | 9.76e-02 | 9.54e-02 | 9.61e-02 | 5.25e+00 | 5.86e+00 | 5.55e+00 | 4.63e-03 | 7.14e-03 | 5.76e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 7331265 | 7332191 | FBgn0261848 | 0.3970 | - | CG42780 | protein_coding | 2.78e-10 | 5.05e-08 | -4.70044 | 5.32e+00 | 5.58e+00 | 4.00e+00 | 3.00e-02 | 3.62e-02 | 1.16e-02 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 7.70e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 20528503 | 20529464 | FBgn0050151 | 0.4459 | - | CG30151 | protein_coding | 2.79e-10 | 5.05e-08 | 4.08099 | 6.13e+00 | 6.11e+00 | 5.49e+00 | 6.34e-02 | 6.25e-02 | 4.04e-02 | 1.01e+01 | 9.97e+00 | 1.00e+01 | 9.88e-01 | 9.23e-01 | 9.49e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 20925891 | 20949512 | FBgn0011591 | 0.4372 | - | fng | protein_coding | 3.49e-10 | 6.18e-08 | 4.68450 | 1.00e+00 | 2.00e+00 | 0.00e+00 | 5.61e-04 | 1.68e-03 | 0.00e+00 | 5.58e+00 | 6.02e+00 | 6.07e+00 | 2.63e-02 | 3.59e-02 | 3.70e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 18387084 | 18390344 | FBgn0022355 | 0.5149 | + | Tsf1 | protein_coding | 5.23e-10 | 9.03e-08 | 3.99367 | 6.75e+00 | 7.48e+00 | 6.83e+00 | 8.00e-02 | 1.32e-01 | 8.45e-02 | 1.11e+01 | 1.12e+01 | 1.08e+01 | 1.66e+00 | 1.73e+00 | 1.37e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 7651180 | 7651900 | FBgn0035806 | 0.4840 | + | PGRP-SD | protein_coding | 5.54e-10 | 9.34e-08 | 4.16189 | 0.00e+00 | 3.81e+00 | 2.32e+00 | 0.00e+00 | 1.15e-02 | 3.53e-03 | 6.95e+00 | 6.97e+00 | 6.77e+00 | 1.08e-01 | 1.09e-01 | 9.52e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 18867391 | 18867895 | FBgn0034407 | 0.4752 | + | DptB | protein_coding | 6.97e-10 | 1.15e-07 | 4.09917 | 4.17e+00 | 6.13e+00 | 5.39e+00 | 1.28e-02 | 5.19e-02 | 3.08e-02 | 8.31e+00 | 9.11e+00 | 1.04e+01 | 2.38e-01 | 4.16e-01 | 1.02e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 3965435 | 3968655 | FBgn0029689 | 0.4728 | - | CG6428 | protein_coding | 7.18e-10 | 1.16e-07 | -3.88486 | 8.64e+00 | 8.23e+00 | 8.10e+00 | 2.40e-01 | 1.80e-01 | 1.65e-01 | 4.09e+00 | 4.46e+00 | 4.75e+00 | 9.64e-03 | 1.27e-02 | 1.57e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 17767165 | 17767786 | FBgn0034278 | 0.3971 | - | CG14488 | protein_coding | 7.50e-10 | 1.17e-07 | 4.52356 | 1.00e+00 | 2.32e+00 | 0.00e+00 | 7.26e-04 | 2.90e-03 | 0.00e+00 | 5.81e+00 | 6.04e+00 | 5.95e+00 | 3.99e-02 | 4.72e-02 | 4.43e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 20534245 | 20535835 | FBgn0034512 | 0.4569 | + | CG18067 | protein_coding | 7.63e-10 | 1.17e-07 | 3.84597 | 8.12e+00 | 8.61e+00 | 7.79e+00 | 1.55e-01 | 2.18e-01 | 1.23e-01 | 1.22e+01 | 1.20e+01 | 1.20e+01 | 2.55e+00 | 2.31e+00 | 2.30e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 30185423 | 30191252 | FBgn0039754 | 0.4655 | - | CG9747 | protein_coding | 7.93e-10 | 1.19e-07 | 3.94251 | 3.58e+00 | 3.91e+00 | 2.32e+00 | 6.49e-03 | 8.25e-03 | 2.36e-03 | 7.27e+00 | 7.59e+00 | 7.18e+00 | 9.02e-02 | 1.13e-01 | 8.49e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 2307948 | 2308872 | FBgn0031412 | 0.3968 | + | CG16995 | protein_coding | 9.81e-10 | 1.45e-07 | 3.82200 | 3.91e+00 | 3.46e+00 | 1.00e+00 | 9.49e-03 | 6.78e-03 | 6.78e-04 | 7.18e+00 | 6.97e+00 | 6.98e+00 | 9.76e-02 | 8.40e-02 | 8.47e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 2285925 | 2286873 | FBgn0051681 | 0.4078 | - | CG31681 | protein_coding | 1.12e-09 | 1.61e-07 | -4.49825 | 3.58e+00 | 4.52e+00 | 6.29e+00 | 9.79e-03 | 1.96e-02 | 6.85e-02 | 1.00e+00 | 1.00e+00 | 0.00e+00 | 8.90e-04 | 8.90e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 15508896 | 15509917 | FBgn0264775 | 0.4266 | - | CG44013 | protein_coding | 1.62e-09 | 2.29e-07 | 3.74869 | 7.81e+00 | 7.99e+00 | 7.89e+00 | 1.45e-01 | 1.65e-01 | 1.54e-01 | 1.15e+01 | 1.16e+01 | 1.18e+01 | 1.88e+00 | 2.08e+00 | 2.31e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 22597245 | 22600695 | FBgn0034741 | 0.4005 | + | CG4269 | protein_coding | 2.65e-09 | 3.68e-07 | 3.86481 | 6.09e+00 | 6.64e+00 | 5.64e+00 | 3.80e-02 | 5.62e-02 | 2.78e-02 | 1.02e+01 | 1.01e+01 | 9.88e+00 | 6.56e-01 | 6.10e-01 | 5.33e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 20533359 | 20533934 | FBgn0050154 | 0.3976 | + | CG30154 | protein_coding | 2.83e-09 | 3.85e-07 | 4.13614 | 2.00e+00 | 2.58e+00 | 1.00e+00 | 1.93e-03 | 3.22e-03 | 6.44e-04 | 6.51e+00 | 5.86e+00 | 5.95e+00 | 5.79e-02 | 3.67e-02 | 3.93e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 8396397 | 8411767 | FBgn0033289 | 0.4390 | - | CG2121 | protein_coding | 6.10e-09 | 8.13e-07 | 4.93860 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 5.39e+00 | 4.64e+00 | 4.64e+00 | 2.82e-02 | 1.65e-02 | 1.65e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 6199216 | 6199891 | FBgn0262536 | 0.3476 | - | CG43090 | protein_coding | 6.21e-09 | 8.13e-07 | -3.67243 | 5.21e+00 | 6.21e+00 | 5.39e+00 | 2.69e-02 | 5.45e-02 | 3.06e-02 | 1.00e+00 | 2.58e+00 | 2.00e+00 | 7.47e-04 | 3.73e-03 | 2.24e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3R | 15402598 | 15407070 | FBgn0038337 | 0.4375 | - | CG6125 | protein_coding | 6.53e-09 | 8.40e-07 | 3.62414 | 7.21e+00 | 7.19e+00 | 7.18e+00 | 8.62e-02 | 8.50e-02 | 8.44e-02 | 1.07e+01 | 1.09e+01 | 1.08e+01 | 9.85e-01 | 1.13e+00 | 1.05e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2L | 9736645 | 9737949 | FBgn0032140 | 0.5218 | + | CG13117 | protein_coding | 1.26e-08 | 1.59e-06 | 3.59054 | 3.46e+00 | 4.46e+00 | 3.32e+00 | 5.25e-03 | 1.10e-02 | 4.72e-03 | 7.41e+00 | 7.26e+00 | 7.61e+00 | 8.87e-02 | 7.97e-02 | 1.02e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 23600914 | 23601773 | FBgn0067903 | 0.4767 | - | IM18 | protein_coding | 1.51e-08 | 1.82e-06 | 3.57191 | 3.81e+00 | 5.25e+00 | 5.88e+00 | 9.89e-03 | 2.81e-02 | 4.41e-02 | 6.94e+00 | 8.22e+00 | 9.81e+00 | 9.28e-02 | 2.27e-01 | 6.82e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 23600914 | 23601773 | FBgn0260455 | 0.4767 | - | CG10332 | protein_coding | 1.51e-08 | 1.82e-06 | 3.57191 | 3.81e+00 | 5.25e+00 | 5.88e+00 | 7.94e-03 | 2.26e-02 | 3.54e-02 | 6.94e+00 | 8.22e+00 | 9.81e+00 | 7.45e-02 | 1.82e-01 | 5.48e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2R | 20531867 | 20532969 | FBgn0265862 | 0.4116 | + | CR44651 | lincRNA | 1.51e-08 | 1.82e-06 | 4.49825 | 1.00e+00 | 1.00e+00 | 0.00e+00 | 7.84e-04 | 7.84e-04 | 0.00e+00 | 6.09e+00 | 4.25e+00 | 4.70e+00 | 5.25e-02 | 1.41e-02 | 1.96e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 6259105 | 6262694 | FBgn0001258 | 0.4370 | - | ImpL3 | protein_coding | 1.57e-08 | 1.85e-06 | 3.57274 | 4.39e+00 | 4.81e+00 | 4.91e+00 | 1.04e-02 | 1.41e-02 | 1.51e-02 | 8.01e+00 | 8.61e+00 | 8.19e+00 | 1.34e-01 | 2.03e-01 | 1.52e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3L | 10623066 | 10623576 | FBgn0260396 | 0.4560 | - | CG42521 | protein_coding | 1.75e-08 | 2.04e-06 | -3.49399 | 3.81e+00 | 6.17e+00 | 6.38e+00 | 9.65e-03 | 5.27e-02 | 6.09e-02 | 0.00e+00 | 3.17e+00 | 2.32e+00 | 0.00e+00 | 5.94e-03 | 2.97e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Byn_vs_Ras.Download the whole result list for Byn_vs_Ras.Download the raw read counts table for the experiment.Download the normalized read counts table for the experiment.
References
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