| Previous changeset 2:cb133602cd9b (2018-05-30) Next changeset 4:90fe78a19b55 (2018-11-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce |
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modified:
chipseeker.R chipseeker.xml test-data/out.int test-data/out.pdf test-data/outflank.tab test-data/outint.int test-data/outint.tab test-data/outtss.tab |
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added:
test-data/out.rdata |
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| diff -r cb133602cd9b -r 535321abf9a4 chipseeker.R --- a/chipseeker.R Wed May 30 06:12:27 2018 -0400 +++ b/chipseeker.R Fri Jun 01 02:13:33 2018 -0400 |
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| @@ -6,6 +6,7 @@ suppressPackageStartupMessages({ library(ChIPseeker) library(GenomicFeatures) + library(rtracklayer) library(optparse) }) @@ -17,7 +18,8 @@ make_option(c("-F","--flankgeneinfo"), type="logical", help="Add flanking gene info"), make_option(c("-D","--flankgenedist"), type="integer", help="Flanking gene distance"), make_option(c("-f","--format"), type="character", help="Output format (interval or tabular)."), - make_option(c("-p","--plots"), type="character", help="PDF of plots.") + make_option(c("-p","--plots"), type="logical", help="PDF of plots."), + make_option(c("-r","--rdata"), type="logical", help="Output RData file.") ) parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) @@ -28,7 +30,6 @@ up = args$upstream down = args$downstream format = args$format -plots = args$plots peaks <- readPeakFile(peaks) @@ -40,25 +41,32 @@ peakAnno <- annotatePeak(peaks, TxDb=txdb, tssRegion=c(-up, down)) } +# Add gene name +features <- import(gtf, format="gtf") +ann <- unique(mcols(features)[, c("gene_id", "gene_name")]) +res <- as.data.frame(peakAnno) +res <- merge(res, ann, by.x="geneId", by.y="gene_id") +names(res)[names(res) == "gene_name"] <- "geneName" + +#Extract metadata cols, 1st is geneId, rest should be from col 7 to end +metacols <- res[, c(7:ncol(res), 1)] # Convert from 1-based to 0-based format -res <- as.GRanges(peakAnno) -metacols <- mcols(res) if (format == "interval") { metacols <- apply(as.data.frame(metacols), 1, function(col) paste(col, collapse="|")) - resout <- data.frame(Chrom=seqnames(res), - Start=start(res) - 1, - End=end(res), + resout <- data.frame(Chrom=res$seqnames, + Start=res$start - 1, + End=res$end, Comment=metacols) } else { - resout <- data.frame(Chrom=seqnames(res), - Start=start(res) - 1, - End=end(res), + resout <- data.frame(Chrom=res$seqnames, + Start=res$start - 1, + End=res$end, metacols) } write.table(resout, file="out.tab", sep="\t", row.names=FALSE, quote=FALSE) -if (!is.null(plots)) { +if (!is.null(args$plots)) { pdf("out.pdf", width=14) plotAnnoPie(peakAnno) plotAnnoBar(peakAnno) @@ -66,4 +74,10 @@ upsetplot(peakAnno) plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS") dev.off() +} + +## Output RData file + +if (!is.null(args$rdata)) { + save.image(file = "ChIPseeker_analysis.RData") } \ No newline at end of file |
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| diff -r cb133602cd9b -r 535321abf9a4 chipseeker.xml --- a/chipseeker.xml Wed May 30 06:12:27 2018 -0400 +++ b/chipseeker.xml Fri Jun 01 02:13:33 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="chipseeker" name="ChIPseeker" version="1.14.2.1">\n+<tool id="chipseeker" name="ChIPseeker" version="1.14.2.2">\n <description>for ChIP peak annotation and visualization</description>\n <requirements>\n <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement>\n@@ -31,6 +31,7 @@\n #end if\n -f $format\n -p $pdf\n+ -r $rdata\n ]]>\n </command>\n <inputs>\n@@ -58,6 +59,9 @@\n </param>\n <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />\n <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />\n+ <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"\n+ help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">\n+ </param>\n \n <section name="adv" expanded="false" title="Advanced Options">\n <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." />\n@@ -79,15 +83,19 @@\n <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">\n <filter>rscript</filter>\n </data>\n+ <data name="out_rdata" format="rdata" from_work_dir="ChIPseeker_analysis.RData" label="${tool.name} on ${on_string}: RData file">\n+ <filter>rdata</filter>\n+ </data>\n </outputs>\n \n <tests>\n <!-- Ensure bed and GTF inputs and all outputs work -->\n- <test expect_num_outputs="3">\n+ <test expect_num_outputs="4">\n <param name="peaks" value="in.bed" ftype="bed"/>\n <param name="gtf_source_select" value="history"/>\n <param name="gtf_hist" value="in.gtf"/>\n <param name="rscript" value="True"/>\n+ <param name="rdata" value="True"/>\n <output name="out_tab" ftype="interval" file="out.int" />\n <output name="out_plots" file="out.pdf" compare="sim_size"/>\n <output name="out_rscript" >\n@@ -95,6 +103,7 @@\n <has_text_matching expression="peakAnno.*annotatePeak" />\n </assert_contents>\n </output>\n+ <output name="out_rdata" file="out.rdata" compare="sim_size" />\n </test>\n <!-- Ensure built-in GTF works -->\n <test expect_num_outputs="2">\n@@ -170,7 +179,7 @@\n 18 371109 372102 DiffBind 0 .\n ===== ====== ====== ======== ===== ======\n \n-A GTF file for annotation.\n+A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name".\n \n -----\n \n@@ -180,7 +189,11 @@\n \n * a file of annotated peaks in Interval or Tabular format\n * a PDF of plots (plotAnnoPie, vennpie, upsetplot)\n+\n+Optionally, you can choose to output\n+\n * the R script used by this tool\n+ * an RData file\n \n **Annotated peaks**\n \n@@ -191,11 +204,11 @@\n ===== ====== ====== =====================================================================================================================================================\n Chrom Start End Comment\n ===== ====== ====== =====================================================================================================================================================\n- 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869\n- 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1'..b'== =============== =============== =============\n- 18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 3869\n- 18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENSG00000263006 ENST00000608049 0\n- 18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 53040\n- 18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 0\n- 18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 28280\n- ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== =============\n+ ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============\n+ Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId\n+ ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============\n+ 18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 3869 COLEC12 ENSG00000158270\n+ 18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENST00000400256 53040 COLEC12 ENSG00000158270\n+ 18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENST00000400256 0 COLEC12 ENSG00000158270\n+ 18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 28280 COLEC12 ENSG00000158270\n+ 18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENST00000608049 0 ROCK1P1 ENSG00000263006\n+ ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============\n \n .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html\n .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html\n' |
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| diff -r cb133602cd9b -r 535321abf9a4 test-data/out.int --- a/test-data/out.int Wed May 30 06:12:27 2018 -0400 +++ b/test-data/out.int Fri Jun 01 02:13:33 2018 -0400 |
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| @@ -1,6 +1,6 @@ Chrom Start End Comment -18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869 -18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENSG00000263006|ENST00000608049| 0 -18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|53040 -18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 0 -18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|28280 +18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256| 3869|COLEC12|ENSG00000158270 +18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENST00000400256|53040|COLEC12|ENSG00000158270 +18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270 +18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256|28280|COLEC12|ENSG00000158270 +18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006 |
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| diff -r cb133602cd9b -r 535321abf9a4 test-data/out.pdf |
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| Binary file test-data/out.pdf has changed |
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| diff -r cb133602cd9b -r 535321abf9a4 test-data/out.rdata |
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| Binary file test-data/out.rdata has changed |
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| diff -r cb133602cd9b -r 535321abf9a4 test-data/outflank.tab --- a/test-data/outflank.tab Wed May 30 06:12:27 2018 -0400 +++ b/test-data/outflank.tab Fri Jun 01 02:13:33 2018 -0400 |
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| @@ -1,6 +1,6 @@ -Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS flank_txIds flank_geneIds flank_gene_distances -18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 3869 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 -18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENSG00000263006 ENST00000608049 0 ENST00000608049 ENSG00000263006 0 -18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 53040 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 -18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 0 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 -18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 28280 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 +Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS flank_txIds flank_geneIds flank_gene_distances geneName geneId +18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 3869 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 COLEC12 ENSG00000158270 +18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENST00000400256 53040 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 COLEC12 ENSG00000158270 +18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENST00000400256 0 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 COLEC12 ENSG00000158270 +18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 28280 ENST00000400256;ENST00000582147 ENSG00000158270;ENSG00000158270 0;0 COLEC12 ENSG00000158270 +18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENST00000608049 0 ENST00000608049 ENSG00000263006 0 ROCK1P1 ENSG00000263006 |
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| diff -r cb133602cd9b -r 535321abf9a4 test-data/outint.int --- a/test-data/outint.int Wed May 30 06:12:27 2018 -0400 +++ b/test-data/outint.int Fri Jun 01 02:13:33 2018 -0400 |
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| @@ -1,6 +1,6 @@ Chrom Start End Comment -18 394599 396513 DiffBind|0|.|1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869 -18 111566 112005 DiffBind|0|.|439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06|Promoter (<=1kb)|1|111568|112005| 438|1|ENSG00000263006|ENST00000608049| 0 -18 346463 347342 DiffBind|0|.|879|5|5.77|3.24|2.52|6.51e-06|0.00303|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|53040 -18 399013 400382 DiffBind|0|.|1369|7.62|7|8.05|-1.04|1.04e-05|0.00364|Promoter (<=1kb)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 0 -18 371109 372102 DiffBind|0|.|993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|28280 +18 394599 396513 DiffBind|0|.|1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256| 3869|COLEC12|ENSG00000158270 +18 346463 347342 DiffBind|0|.|879|5|5.77|3.24|2.52|6.51e-06|0.00303|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENST00000400256|53040|COLEC12|ENSG00000158270 +18 399013 400382 DiffBind|0|.|1369|7.62|7|8.05|-1.04|1.04e-05|0.00364|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270 +18 371109 372102 DiffBind|0|.|993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256|28280|COLEC12|ENSG00000158270 +18 111566 112005 DiffBind|0|.|439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006 |
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| diff -r cb133602cd9b -r 535321abf9a4 test-data/outint.tab --- a/test-data/outint.tab Wed May 30 06:12:27 2018 -0400 +++ b/test-data/outint.tab Fri Jun 01 02:13:33 2018 -0400 |
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| @@ -1,6 +1,6 @@ -Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS -18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 3869 -18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENSG00000263006 ENST00000608049 0 -18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 53040 -18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 0 -18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 28280 +Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId +18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 3869 COLEC12 ENSG00000158270 +18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENST00000400256 53040 COLEC12 ENSG00000158270 +18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENST00000400256 0 COLEC12 ENSG00000158270 +18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 28280 COLEC12 ENSG00000158270 +18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENST00000608049 0 ROCK1P1 ENSG00000263006 |
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| diff -r cb133602cd9b -r 535321abf9a4 test-data/outtss.tab --- a/test-data/outtss.tab Wed May 30 06:12:27 2018 -0400 +++ b/test-data/outtss.tab Fri Jun 01 02:13:33 2018 -0400 |
| b |
| @@ -1,6 +1,6 @@ -Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS -18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 3869 -18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter 1 111568 112005 438 1 ENSG00000263006 ENST00000608049 0 -18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 53040 -18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 0 -18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 28280 +Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId +18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 3869 COLEC12 ENSG00000158270 +18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENST00000400256 53040 COLEC12 ENSG00000158270 +18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter 1 346465 400382 53918 2 ENST00000400256 0 COLEC12 ENSG00000158270 +18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 28280 COLEC12 ENSG00000158270 +18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter 1 111568 112005 438 1 ENST00000608049 0 ROCK1P1 ENSG00000263006 |