GTF separate coding and non-coding exons

Question

[igor]

Is there a way to keep coding and remove non-coding regions in a GTF file? UTRs are non-coding and CDSs are coding, so the regions are [usually] well-defined, but some tools look at exons. However, exons can be both. Is there a way to break up and extract coding exons?

The easiest solution I can think of is to remove all UTRs and exons, then copy CDSs and rename them exon. Not sure if I may be overlooking something there.

Answer 1

[Juke34]

Your solution works perfectly fine. I usual do the same in similar cases.

If you have mRNA features and gene features you may modify their start and stop accordingly in order to keep a coherent information.