I have two annotations of the same genome generated with different annotation pipelines. I want to identify overlapping gene models.
An important feature of this genome is that there are many 'genes within genes', i.e. a genemodel in the intron of another genemodel. Therefore, I only want to count two genemodels as overlapping when their coding sequence exon annotations overlap.
Using something like
bedtools intersect it is straightforward to calculate overlap between the gene-level annotations.
However: I am not sure how to select genes as overlapping when only their coding sequence exons (CDS features) overlap.