featureCounts usage #18
Description
Dear @alee @pbanaszkiewicz
I see that in your tutorial, the way featureCounts is being run is using -t gene argument rather than -t exon. However, the former will lead to counting of intronic reads as well (see usage in manual, here, here and here. I believe this was an oversight and could be corrected with the following featureCounts --countReadPairs -t exon -g ID -a ath_annotation.gff3 -o counts.txt mapped/*.bam (feel free to drop --countreadPairs if not using the featureCounts > 2.0 or if the library is SE).
featureCounts -O -t gene -g ID -a ath_annotation.gff3 -o counts.txt mapped/*.bam