I would like to have per-base coverage of a bam file of an RNAseq experiment, but only on exons.
I know how to do that on all genome with bedtools:
bedtools genomecov -d -ibam aligned_reads.bam -g genome.fa > cov.txt
And I have a gff file giving me the position of exons on my species.
Does anyone know a way to have the same result, but only on given exon positions?