Could you help me to convert GFF3 to GTF to use it in featureCounts? I can not figure out how to use gffread. Thanks.
If the GTF version is available, use that instead of trying to covert it over. There isn’t only one way to do the conversion, and it doesn’t work well on all GFF3 data from my experience.
Two things to make sure to do are:
- Input a GFF3 that does not contain sequences at the end
- Set the option “Feature File Output” → “GTF”
If that isn’t enough help, please put a copy of the GFF3 into a new history, then generate a share a link to that history and post it back. You can include your attempts in the same history as a reference.
Thanks! It works great.
It did not work at the beginning, I just found out about the issue. It did not work with a compressed file, which NCBI provides. Unzip it, and then everything works fine. Thanks.