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!

"+ "

Usage example:

"+ "
" +
 "java -jar picard.jar CollectRnaSeqMetrics \\
" +