This is a test version of Biostars. For the public version, visit https://www.biostars.org.
STAR => featureCounts pipeline

Hello,

I'm looking at STAR's --quantMode TranscriptomeSAM option, and am puzzled, should I use TranscriptomeSAM for input into featureCounts, or should I use the Aligned.sortedByCoordinate.out.bam file output by STAR for input into featureCounts?

I already get the counts from --quantMode GeneCounts I don't see the purpose of TranscriptomeSAM.

thanks

rna-seq
• 6,234 views • link
updated by h.mon h.mon • written by dec986 dec986

1 answer

--quantMode TranscriptomeSAM is to be used with RSEM / eXpress / Salmon, for isoform quantification. If you want to use featureCounts, use Aligned.sortedByCoordinate.out.bam. However, the results of featureCounts should be very similar to --quantMode GeneCounts.

• 0 views • link
written by h.mon h.mon

Log in to answer this question.

More posts like this