Hi, this seems like quite a straightforward question so apologies if it has been asked before (I couldn't find anything similar). I have a .gtf file containing CDS coordinates for a chromosome, and I plan to extract codons containing 4d sites. Therefore I would like to remove any CDS that overlap (on the same, or opposite, strand) so there is no ambiguity about what is a 4d site and what isn't. I've been trying to do this with bedtools but I'm not having much luck, as intersect would need to have an option where features that overlap 100% are ignored for me to compare the file to itself. Thanks
-r 1does not work?
Hi, thanks for your answer. Do you mean
-v -f 1 -r? This gives me zero output as every CDS is overlapped 100%.