STAR => featureCounts pipeline
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4.4 years ago
dec986 ▴ 340

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 • 4.2k views
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Entering edit mode
4.4 years ago
h.mon 34k

--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.

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