Merging RNA modifications with transcript features.
I would like some clarification on how to correctly intersect RNA modifications with transcript features. I have a bed file with extracted modifications from modkit. I would like to intersect these modifications with transcript feature beds like cds.bed, 3utr. bed (extracted from gtf file). How do I use bedtools intersect so that each modification is mapped only once per transcript feature?
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What commands have you tried, and what is wrong with the output?
The number of modifications in the output file are more than expected
That command looks appropriate for what you are suggesting. Why do you think there are more modifications than expected? Please note that genes with multiple alleles will each have a entry in the output
.bedfile, assuming there is a modification on a shared exon.As a proof of concept, you can get filter to only retain gene level annotations in the bed file, then run this command and see if the numbers match. But there also may be gene annotations with overlapping start and end sites which can inflate the values too.
Thank you! Do you perhaps know how to deal with gene annotations with overlapping start and end sites?