In the FeatureCounts->advanced setting-> GFF feature type filter, the default is exon, but if change to intron, the values are the same, and if leave it blank, it still the same. So it looks like this function do not work. I need to get the counts for the whole gene (GRO-seq), including UTR, exon, and intron, how can I do that?
which annotation file are you using? I checked the wrapper, and it seems to work fine.