I have a list of exons (in BED format) and I wish to find the coverage per exon from a BAM file. I was looking at Bedtools coverageBED but I don't think that gives me the per exon coverage.
Are there any suggestions on how I should go about calculating the coverage of each exon?
Also, eventually, I have to also calculate per gene coverage. How do I go about calculating the per gene coverage from the per exon coverage obtained above ? Do I simply take the average of the coverage across all exons of the gene?
What type of data are these? RNA-seq? Exome capture? Genomic DNA? And what are you going to do with the coverage numbers?