STAR => featureCounts pipeline

Question

[dec986]

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

Answer 1

[h.mon]

--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.