I was trying featureCounts for with these 2 following settings.
featureCounts -t exon -g gene_id (the rest default, not specified)
featureCounts -t gene -g gene_id (the rest default, not specified)
I expected to see more reads (fragments) in condition 2, since the region of "gene" in the annotation gtf covers both "exon" and intron region. However, it's surprising to see that for a lot of the genes i got more counts in condition 1. Could anybody help with this? Thanks in advance!