I have some bam files aligned to mouse reference genome. I want to analyze some motif enrichment in the 3'UTR of this samples but I realize that some mRNA have longer 3'UTR than the reference genome. I double checked this an is something reported in platelets that is what I'm working.
Is there any way to get the full 3'UTR using, for example coverage and expand the preexistent 3'UTR bed file? I was thinking on a kind of loop that check coverage every 100bp and, if coverage is > threshold, append the sequence... Any other ideas? Actually I am not quite sure that the previous idea would work...