Counting reads in CDS - but skipping few first/last codons
I've been struggling with this for some time now, and finally decided to ask you guys for advice: I'm trying to analyze some ribosome profiling data, and would like to count reads (e.g. using HT-Seq) in cds, but at the same time I'd like to exclude several first and last codons (I think in general people skip first 15 and last 5 codons). I suppose I could potentially achieve this by modifying my gtf? Are there any tools you could recommend I use to get this done? Or do you have any other ideas/suggestions on how I start with this? Thank you for your help.
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I think bedtools can be used to change the gtf.
More specifically:
bedtools slopis able to increase the size of features. However, using negative integers for-land-rshrinks features at the desired end.Thanks! So in this case proper way would be to extract CDS exons containing start codons, resize, and then merge back? Thanks again!