I am using
featureCounts to count the number of reads mapping to genes.
featureCounts -a $myGTF \ -o counted_output \ -R BAM Aligned.sortedByCoord.out.bam \ -T $NUMCORES \ -M
The above bash command works counting reads that map to the exonic sequences of each genes annotated in the
My question is, how can I get
featureCounts to also count reads mapping to intronic sequences? It is unclear to me how to achieve this from the documentation but it might be through some combination of