# HG changeset patch # User lparsons # Date 1462307817 14400 # Node ID f242ee1032770958f8cc15f5a57e5d2bf8659f7c # Parent 6b33e31bda1090c1008ce24ad1e76c722d66d7f0 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee diff -r 6b33e31bda10 -r f242ee103277 README.txt --- a/README.txt Thu Jul 16 17:43:43 2015 -0400 +++ b/README.txt Tue May 03 16:36:57 2016 -0400 @@ -16,9 +16,8 @@ The RSeQC package and associated documentation can be found at: http://rseqc.sourceforge.net/ -The galaxy wrapper code was written by +The galaxy wrapper code was written by Nilesh Kavthekar, School of Engineering and Applied Sciences, University of Pennsylvania, Class of 2016 -Modified by +Modified by Lance Parsons, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Bjorn Gruning, University of Freiburg, bjoern.gruening@gmail.com -The development of the wrapper code is housed on BitBucket at: https://bitbucket.org/lance_parsons/rseqc_galaxy_wrapper diff -r 6b33e31bda10 -r f242ee103277 RPKM_saturation.xml --- a/RPKM_saturation.xml Thu Jul 16 17:43:43 2015 -0400 +++ b/RPKM_saturation.xml Tue May 03 16:36:57 2016 -0400 @@ -77,17 +77,30 @@ - - - Read coverage over gene body. - + + + Read coverage over gene body. + + + + rseqc_macros.xml + - - rseqc_macros.xml - + + + + + - - - - - + - + - + > input_list.txt && + #end for + geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output + ]]> + - input_list.txt && - #for $i, $additional_input in enumerate($additionalinputs): - #set $index = $i+2 - #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $additional_input.file.display_name) - #set $fname = 'd' + str($index) + '_' + str($safename) + ".bam" - ln -s '$additional_input.file' '${fname}' && - ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' && - echo '${fname}' >> input_list.txt && - #end for - geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output - ]]> - + + + + + - - - - - - - - - - - - - len(additionalinputs) >= 2 - - - - + + + + len(inputs) >= 3 + + + + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - + - `_ + When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap. + Coverage skewness was measured by `Pearson’s skewness coefficients `_ .. image:: http://rseqc.sourceforge.net/_images/geneBody_workflow.png - :width: 800 px - :scale: 80 % + :width: 800 px + :scale: 80 % -Inputs -++++++++++++++ + ## Inputs + + Input BAM/SAM file + Alignment file in BAM/SAM format. -Input BAM/SAM file - Alignment file in BAM/SAM format. + Reference gene model + Gene Model in BED format. -Reference gene model - Gene Model in BED format. - -Minimum mRNA length + Minimum mRNA length Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100). -Outputs -++++++++++++++ -Text + ## Outputs + + Text Table that includes the data used to generate the plots -R Script + R Script R script file that reads the data and generates the plot -PDF + PDF The final plot, in PDF format -Example plots: + Example plots: .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.curves.png - :height: 600 px - :width: 600 px - :scale: 80 % + :height: 600 px + :width: 600 px + :scale: 80 % .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.heatMap.png - :height: 600 px - :width: 600 px - :scale: 80 % + :height: 600 px + :width: 600 px + :scale: 80 % ------ + ## About RSeQC -About RSeQC -+++++++++++ + The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation. -The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation. + The RSeQC package is licensed under the GNU GPL v3 license. -The RSeQC package is licensed under the GNU GPL v3 license. - -.. image:: http://rseqc.sourceforge.net/_static/logo.png + .. image:: http://rseqc.sourceforge.net/_static/logo.png -.. _RSeQC: http://rseqc.sourceforge.net/ -]]> - + .. _RSeQC: http://rseqc.sourceforge.net/ + ]]> + - + diff -r 6b33e31bda10 -r f242ee103277 junction_saturation.xml --- a/junction_saturation.xml Thu Jul 16 17:43:43 2015 -0400 +++ b/junction_saturation.xml Tue May 03 16:36:57 2016 -0400 @@ -50,6 +50,7 @@ + diff -r 6b33e31bda10 -r f242ee103277 read_quality.xml --- a/read_quality.xml Thu Jul 16 17:43:43 2015 -0400 +++ b/read_quality.xml Tue May 03 16:36:57 2016 -0400 @@ -36,16 +36,12 @@ - 3')",ylab="Phred Quality Score",outline=F) dev.off() pdf('output.qual.heatmap.pdf') 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+qual=c(119,0,0,0,2,3,2,5,6,8,6,2,0,3,11,16,6,26,11,13,25,39,7,40,33,33,58,51,116,87,55,256,54,323,263,140,812,654,1119,105,0,0,0,2,2,2,4,8,6,21,3,1,1,8,13,13,16,16,14,29,32,18,50,30,57,66,73,97,105,60,253,57,330,270,142,801,630,1069,109,0,1,0,1,3,2,7,11,14,13,2,4,3,8,14,21,27,17,14,26,39,11,37,28,74,64,55,86,106,62,234,56,326,269,147,787,645,1081,108,0,0,0,1,6,4,2,9,12,7,0,3,3,9,14,13,24,20,8,24,46,14,43,28,59,67,75,88,107,51,285,56,293,239,139,802,660,1084,97,0,1,0,1,0,3,9,8,11,5,4,2,4,10,16,19,24,7,8,35,43,19,49,29,51,67,51,93,107,43,306,65,345,223,123,789,661,1075,96,0,0,0,3,0,2,5,11,6,8,2,7,2,12,17,15,16,12,11,25,31,12,32,36,59,70,69,74,99,56,277,59,343,249,111,845,650,1081,86,0,0,0,2,4,2,6,12,8,10,1,7,7,9,11,14,26,14,9,14,53,17,34,41,55,71,76,76,117,62,238,62,339,229,155,798,607,1131,76,0,0,0,1,4,4,6,11,9,13,5,5,6,6,17,19,20,17,8,19,45,15,30,33,60,68,58,76,99,59,291,54,349,251,129,818,602,1120,74,0,0,1,2,3,1,5,6,6,7,7,2,4,11,11,16,24,13,9,24,48,19,33,39,63,67,68,78,104,66,284,62,329,240,147,749,649,1132,98,0,0,0,1,2,2,6,11,19,10,0,5,3,8,18,19,24,14,5,18,53,21,41,39,56,79,64,70,93,57,291,42,334,259,143,795,616,1087,71,0,0,0,3,3,4,3,5,6,7,2,3,5,13,14,6,17,21,12,27,40,16,34,39,46,64,78,103,103,63,279,37,314,239,118,805,674,1129,76,1,0,0,4,3,3,7,10,11,8,5,6,3,12,13,18,21,16,18,21,46,21,32,41,77,56,77,103,105,54,269,40,320,247,144,796,621,1098,87,0,0,0,3,2,1,7,12,8,6,5,13,8,11,9,16,23,13,14,22,40,21,53,48,51,59,77,84,126,75,282,48,306,254,151,808,586,1074,76,0,0,0,5,1,3,6,3,7,8,4,3,10,12,14,13,23,12,19,25,43,17,52,42,63,57,92,91,114,61,281,45,342,256,132,812,586,1073,81,0,0,0,1,5,4,4,10,11,9,3,5,5,6,18,21,29,26,14,27,51,17,54,47,51,65,84,84,118,66,291,46,316,244,149,782,579,1080,87,0,0,1,2,5,2,10,17,12,9,0,7,2,10,10,12,20,18,21,27,50,17,50,54,42,82,57,84,103,54,285,41,342,265,115,822,582,1085,118,0,0,0,0,4,3,7,7,11,10,5,6,8,11,18,19,30,34,13,34,47,14,62,49,55,83,82,96,101,51,283,45,346,249,152,843,521,985,73,0,0,0,2,5,6,7,9,11,7,5,4,11,19,13,15,33,18,17,42,57,25,46,65,67,94,68,93,117,67,279,53,306,295,132,844,504,993,72,0,0,1,2,3,5,4,16,13,14,2,8,2,18,19,27,37,27,18,29,57,21,47,57,62,87,81,89,111,57,293,49,319,270,142,858,495,990,78,0,0,1,1,5,3,3,13,10,13,5,7,5,14,15,24,30,23,23,24,57,19,72,49,70,70,72,91,124,60,298,52,347,270,147,841,486,980,71,0,0,0,4,5,3,10,9,10,12,5,9,6,23,14,19,33,27,21,34,60,16,47,57,55,82,84,109,117,44,305,45,335,265,146,856,510,954,80,0,0,0,5,4,5,4,6,10,7,4,0,11,14,19,18,32,25,29,32,75,19,58,56,66,81,79,102,133,52,332,44,306,260,152,879,486,917,80,0,0,0,2,5,2,11,11,13,4,4,5,8,12,15,21,34,27,18,44,58,26,72,62,72,90,84,97,137,51,324,54,332,254,143,857,492,881,78,0,0,0,3,4,1,9,9,3,8,9,9,5,12,20,19,37,30,23,38,69,29,64,51,71,95,92,99,133,52,320,51,340,275,152,868,467,856,73,0,0,0,1,2,3,6,14,19,7,3,3,10,24,15,26,38,27,15,34,71,17,62,72,75,86,84,108,128,65,304,41,356,239,139,864,494,876,100,0,1,1,6,3,6,14,19,11,9,7,11,5,8,25,21,35,16,18,39,61,19,65,42,62,91,83,80,105,38,318,50,372,289,135,847,504,884,72,0,0,1,1,4,2,12,10,17,11,5,3,3,21,25,29,34,34,19,38,55,20,55,59,82,96,99,106,133,45,299,71,339,265,157,822,474,882,73,0,0,0,1,2,5,3,17,16,6,5,7,11,7,16,14,30,31,16,45,71,29,50,62,72,78,77,107,132,62,273,47,366,277,161,892,462,877,91,0,0,0,3,2,2,7,10,6,9,9,6,11,15,17,19,33,20,10,30,54,20,68,48,73,84,72,114,131,60,321,60,356,270,159,874,496,840,92,0,0,1,5,5,4,6,8,7,10,4,7,7,16,26,24,33,20,22,36,49,15,53,65,71,79,80,112,127,63,320,49,359,292,141,837,455,900,105,0,0,1,2,5,4,2,15,8,13,8,6,7,19,24,21,30,22,17,35,53,13,52,61,45,93,74,87,120,60,302,41,331,272,131,877,513,931,117,0,0,0,3,5,3,11,23,24,10,5,7,6,8,13,12,40,18,18,40,41,12,45,57,72,86,71,75,125,68,299,55,302,264,154,874,464,973,120,0,1,0,7,3,4,9,13,19,8,5,3,10,17,25,13,19,18,23,33,49,25,41,51,72,74,56,95,112,60,291,58,281,267,145,916,463,993,89,0,0,1,4,9,13,7,8,7,8,6,8,8,18,20,12,34,26,14,31,50,17,45,65,58,68,77,84,110,66,289,54,284,282,164,871,489,1003,162,0,0,1,3,4,4,14,15,24,17,2,6,9,16,15,20,37,20,12,34,49,12,42,50,54,66,62,81,121,56,265,50,292,258,127,878,506,1015,79,0,0,0,5,1,3,3,13,8,6,0,7,11,15,19,11,17,25,16,34,49,16,37,45,69,72,76,79,101,48,303,38,326,254,140,811,619,1043,78,0,0,0,3,0,4,3,8,5,6,8,6,5,13,18,18,32,19,22,39,43,17,39,45,68,77,74,69,118,47,272,47,332,262,139,833,562,1068,96,0,0,1,3,1,5,5,6,6,8,4,7,3,12,9,18,35,15,24,27,57,20,40,53,70,81,89,91,117,46,262,44,298,251,130,817,588,1059,102,0,0,0,5,0,5,4,10,11,12,3,3,7,8,18,15,22,20,17,20,50,21,46,43,71,70,80,91,110,51,239,34,339,258,119,820,614,1058,100,0,0,0,3,5,3,6,10,12,12,5,5,10,6,21,18,28,14,16,33,38,18,45,56,58,71,65,79,109,57,253,47,310,263,129,854,616,1017,97,0,0,1,4,3,1,5,14,7,11,2,5,2,9,6,19,21,18,21,30,37,22,37,64,40,69,53,89,104,66,281,42,355,233,137,771,615,1095,130,0,0,0,5,2,6,10,10,19,20,5,5,4,12,16,17,28,14,12,25,42,16,42,39,57,61,73,84,110,49,261,48,315,254,125,761,643,1028,108,0,2,1,2,1,5,4,12,13,7,6,7,3,6,14,19,20,22,15,22,52,14,50,45,57,67,72,78,119,51,272,45,284,226,127,831,604,1054,124,0,2,2,0,1,2,5,13,17,10,1,6,4,14,11,19,31,14,14,24,30,12,42,41,54,64,74,82,112,68,250,49,308,261,142,775,557,1060,106,0,1,0,1,4,4,10,9,9,7,0,9,6,8,8,16,21,12,18,24,50,14,43,43,56,55,100,87,109,51,261,51,308,217,139,759,562,1041,120,0,0,0,3,3,2,9,7,12,9,6,4,1,10,9,15,26,11,16,22,35,16,26,45,50,60,56,67,74,62,247,50,282,243,123,747,618,1061,116,0,0,0,1,2,3,2,10,15,10,1,2,6,6,10,9,13,8,14,29,26,12,31,42,59,41,57,88,92,58,257,43,304,236,133,707,612,1016,130,0,0,1,2,4,2,6,8,18,21,3,5,5,7,12,15,17,7,7,23,43,9,28,32,44,42,56,68,83,54,225,38,289,181,133,713,594,991,105,0,1,0,0,5,2,6,9,10,23,1,5,3,3,9,9,30,13,7,18,27,12,28,24,49,42,63,75,81,45,226,43,274,217,147,676,571,925,99,0,0,0,0,3,1,3,5,5,16,3,3,6,7,4,13,15,11,3,10,34,16,20,37,46,41,52,66,85,35,201,45,253,201,119,685,497,913,82,0,0,0,0,0,0,0,0,0,2,0,3,5,3,4,5,13,9,5,11,14,3,35,17,21,41,34,67,67,31,184,49,241,167,93,639,515,797) mat=matrix(qual,ncol=51,byrow=F) Lab.palette <- colorRampPalette(c("blue", "orange", "red3","red2","red1","red"), space = "rgb",interpolate=c('spline')) heatmap(mat,Rowv=NA,Colv=NA,xlab="Position of Read",ylab="Phred Quality Score",labRow=seq(from=33,to=71),col = Lab.palette(256),scale="none" ) diff -r 6b33e31bda10 -r f242ee103277 test-data/output.rawCount.xls --- a/test-data/output.rawCount.xls Thu Jul 16 17:43:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -#chr start end name score strand 5% 10% 15% 20% 25% 30% 35% 40% 45% 50% 55% 60% 65% 70% 75% 80% 85% 90% 95% 100% -chr1 17368 17436 NR_106918 0 - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -chr1 17368 17436 NR_107062 0 - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -chr1 34610 36081 NR_026818 0 - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -chr1 69090 70008 NM_001005484 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -chr1 14361 29370 NR_024540 0 - 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 4 4 4 -chr1 34610 36081 NR_026820 0 - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -chr1 11873 14409 NR_046018 0 + 0 0 0 0 0 0 0 0 1 1 1 1 2 2 2 2 2 3 3 3 diff -r 6b33e31bda10 -r f242ee103277 test-data/output.saturation.r --- a/test-data/output.saturation.r Thu Jul 16 17:43:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -pdf('output.saturation.pdf') -par(mfrow=c(2,2)) -name=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95) -S5=c() -S10=c() -S15=c() -S20=c() -S25=c() -S30=c() -S35=c() -S40=c() -S45=c() -S50=c() -S55=c() -S60=c() -S65=c() -S70=c() -S75=c() -S80=c() -S85=c() -S90=c() -S95=c() -boxplot(100*S5,100*S10,100*S15,100*S20,100*S25,100*S30,100*S35,100*S40,100*S45,100*S50,100*S55,100*S60,100*S65,100*S70,100*S75,100*S80,100*S85,100*S90,100*S95,names=name,outline=F,ylab='Percent Relative Error',main='Q1',xlab='Resampling percentage') -name=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95) -S5=c(1.0) -S10=c(1.0) -S15=c(1.0) -S20=c(1.0) -S25=c(1.0) -S30=c(1.0) -S35=c(1.0) -S40=c(1.0) -S45=c(0.259259259259) -S50=c(0.333333333334) -S55=c(0.39393939394) -S60=c(0.444444444444) -S65=c(0.0256410256403) -S70=c(0.0476190476199) -S75=c(0.111111111112) -S80=c(0.166666666666) -S85=c(0.21568627451) -S90=c(0.111111111112) -S95=c(0.0526315789469) -boxplot(100*S5,100*S10,100*S15,100*S20,100*S25,100*S30,100*S35,100*S40,100*S45,100*S50,100*S55,100*S60,100*S65,100*S70,100*S75,100*S80,100*S85,100*S90,100*S95,names=name,outline=F,ylab='Percent Relative Error',main='Q2',xlab='Resampling percentage') -name=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95) -S5=c() -S10=c() -S15=c() -S20=c() -S25=c() -S30=c() -S35=c() -S40=c() -S45=c() -S50=c() -S55=c() -S60=c() -S65=c() -S70=c() -S75=c() -S80=c() -S85=c() -S90=c() -S95=c() -boxplot(100*S5,100*S10,100*S15,100*S20,100*S25,100*S30,100*S35,100*S40,100*S45,100*S50,100*S55,100*S60,100*S65,100*S70,100*S75,100*S80,100*S85,100*S90,100*S95,names=name,outline=F,ylab='Percent Relative Error',main='Q3',xlab='Resampling percentage') -name=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95) -S5=c(4.00000000001) -S10=c(1.5) -S15=c(0.666666666666) -S20=c(1.5) -S25=c(1.00000000001) -S30=c(0.666666666666) -S35=c(0.428571428571) -S40=c(0.25) -S45=c(0.111111111111) -S50=c(0.0) -S55=c(0.09090909091) -S60=c(0.25) -S65=c(0.153846153846) -S70=c(0.0714285714295) -S75=c(0.0) -S80=c(0.0624999999991) -S85=c(0.117647058824) -S90=c(0.111111111111) -S95=c(0.0526315789465) -boxplot(100*S5,100*S10,100*S15,100*S20,100*S25,100*S30,100*S35,100*S40,100*S45,100*S50,100*S55,100*S60,100*S65,100*S70,100*S75,100*S80,100*S85,100*S90,100*S95,names=name,outline=F,ylab='Percent Relative Error',main='Q4',xlab='Resampling percentage') -dev.off() diff -r 6b33e31bda10 -r f242ee103277 test-data/output2.geneBodyCoverage.curves.pdf Binary file test-data/output2.geneBodyCoverage.curves.pdf has changed diff -r 6b33e31bda10 -r f242ee103277 test-data/output2.geneBodyCoverage.heatMap.pdf Binary file test-data/output2.geneBodyCoverage.heatMap.pdf has changed diff -r 6b33e31bda10 -r f242ee103277 test-data/output2.geneBodyCoverage.r --- a/test-data/output2.geneBodyCoverage.r Thu Jul 16 17:43:43 2015 -0400 +++ b/test-data/output2.geneBodyCoverage.r Tue May 03 16:36:57 2016 -0400 @@ -1,8 +1,21 @@ d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam <- c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0) +d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam <- c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0) +d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam <- c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0) +data_matrix <- matrix(c(d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam), byrow=T, ncol=100) +rowLabel <- c("d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam","d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam","d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam") + + +pdf("output.geneBodyCoverage.heatMap.pdf") +rc <- cm.colors(ncol(data_matrix)) +heatmap(data_matrix, scale=c("none"),keep.dendro=F, labRow = rowLabel ,Colv = NA,Rowv = NA,labCol=NA,col=cm.colors(256),margins = c(6, 8),ColSideColors = rc,cexRow=1,cexCol=1,xlab="Gene body percentile (5'->3')", add.expr=x_axis_expr <- axis(side=1,at=c(1,10,20,30,40,50,60,70,80,90,100),labels=c("1","10","20","30","40","50","60","70","80","90","100"))) +dev.off() pdf("output.geneBodyCoverage.curves.pdf") x=1:100 -icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(1) +icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(3) plot(x,d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',xlab="Gene body percentile (5'->3')", ylab="Coverage",lwd=0.8,col=icolor[1]) +lines(x,d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',col=icolor[2]) +lines(x,d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',col=icolor[3]) +legend(0,1,fill=icolor[1:3], legend=c('d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam','d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam','d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam')) dev.off() diff -r 6b33e31bda10 -r f242ee103277 test-data/output2.geneBodyCoverage.txt --- a/test-data/output2.geneBodyCoverage.txt Thu Jul 16 17:43:43 2015 -0400 +++ b/test-data/output2.geneBodyCoverage.txt Tue May 03 16:36:57 2016 -0400 @@ -1,2 +1,4 @@ Percentile 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 diff -r 6b33e31bda10 -r f242ee103277 test-data/pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig Binary file test-data/pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig has changed diff -r 6b33e31bda10 -r f242ee103277 test-data/pairend_strandspecific_51mer_hg19_random.bam Binary file test-data/pairend_strandspecific_51mer_hg19_random.bam has changed diff -r 6b33e31bda10 -r f242ee103277 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jul 16 17:43:43 2015 -0400 +++ b/tool_dependencies.xml Tue May 03 16:36:57 2016 -0400 @@ -1,7 +1,7 @@ - +