diff --git a/src/main/java/picard/analysis/CollectRnaSeqMetrics.java b/src/main/java/picard/analysis/CollectRnaSeqMetrics.java index aed80f0bf..a46e1cd6a 100644 --- a/src/main/java/picard/analysis/CollectRnaSeqMetrics.java +++ b/src/main/java/picard/analysis/CollectRnaSeqMetrics.java @@ -72,11 +72,19 @@ "
The sequence input must be a valid SAM/BAM file containing RNAseq data aligned by an RNAseq-aware genome aligner such a "+ "STAR or TopHat. "+ "The tool also requires a REF_FLAT file, a tab-delimited file containing information about the location of RNA transcripts, "+ -"exon start and stop sites, etc. For more information on the REF_FLAT format, see the following "+ -"description. "+ -"Build-specific REF_FLAT files can be obtained here.
"+ +"exon start and stop sites, etc. For an example refFlat file for GRCh38, see refFlat.txt.gz at "+ +"http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database. "+ +"The first five lines of the tab-limited text file appear as follows."+ -"" + +"DDX11L1 NR_046018 chr1 + 11873 14409 14409 14409 3 11873,12612,13220, 12227,12721,14409," + +"WASH7P NR_024540 chr1 - 14361 29370 29370 29370 11 14361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320, 14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370," + +"DLGAP2-AS1 NR_103863 chr8_KI270926v1_alt - 33083 35050 35050 35050 3 33083,33761,35028, 33281,33899,35050," + +"MIR570 NR_030296 chr3 + 195699400 195699497 195699497 195699497 1 195699400, 195699497," + +"MIR548A3 NR_030330 chr8 - 104484368 104484465 104484465 104484465 1 104484368, 104484465," + +"" + + +"
Note: Metrics labeled as percentages are actually expressed as fractions!
"+ "" + "java -jar picard.jar CollectRnaSeqMetrics \\
" +