how can I count the number of BAM reads falling directly within a set of intervals, given in a GFF format? Note that I do not want reads overlapping the intervals, but ones that fall directly within them.
I tried the following:
intersectBed -abam reads.bam -b exons.gff -wb -f 1
this has redundancies, so I pipe it into coverageBed as follows:
intersectBed -abam reads.bam -b exons.gff -wb -f 1 | coverageBed -abam stdin -b exons.gff
Is this correct? Thanks.