I am trying out something new and am already a little stuck. Any assistance would be really appreciated.
I have whole genome sequencing data for a number of samples, which I have already mapped to the reference assembly for my study species. These are currently in sorted bam files. I would now like to compare sequencing read depth across three 'functional groups'; exons, introns and intergenic regions. My annotations are in a GFF3 file. From reading around I have gathered that I should make three bed files, one pertaining to each functional group.
What I would like to know is how to prepare these bed files using the GFF3 file. Could anyone point me in the right direction?