Annotate CDS and UTR given transcript

Question

[gtho123]

I am annotating a new genome and I am combining several sources of information for the annotation. It combines a de novo annotation as well as lifting over annotations from closely related species.

I have been using GFFCompare (https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) to merge GFF files. This is useful but the combined.gtf file ouput does not carry over CDS (or UTR) annotations. Is there a tool which is similar which retains this information or otherwise is there a tool to add it back in by finding the longest open reading frame within the transcript?

I feel like such a tool probably exists so I thought I'd ask before I go ahead and write my own.

Answer 1

[gtho123]

I switched from GFFCompare to AGAT (https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html) which got around my issue