I have RNA-seq data in a bam file and I have two GRangesLists: one with exons by gene for a subset of genes and one with introns by gene for a subset of genes. I'm trying to calculate the basepair coverage over exons per gene and introns per gene. For any given gene, I'd like to be able to plot basepair coverage in terms of relative exon position (e.g. start of first exon is 1 and if there are 2 100 bp exons, the last number of the x-axis will be 200). I played around a bit with the coverage() function and views based on my two GRangesLists, but it didn't seem like the best way to do this or I was doing something wrong. I was just wondering if anyone has suggestions for how to do this?