Hi Everyone,

I am trying to find out all transcripts that are a subfragment of any other transcript from a gtf file. By subfragment, I mean completely contained in another transcript. I used gffCompare but it does not work, since I compare a particular gtf to itself and gffcompare reports all transcripts as a perfect match. I was wondering if there are some programs that actually report subfragments within a gtf file.

Thanks