How to add exon annotations to genome annotation

Question

[Simone]

I have some annotation files for a few genomes that have CDS, mRNA, and gene entries in the annotation but no exons. How could I add exon annotations for each file? I have the genome file and protein annotation file.

Answer 1

[alex.zaccaron]

You can use AGAT to process your annotation file to add the missing exons. I believe agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o with_exons.gff solves your problem.

[Simone]

Thank you so much! I just discovered AGAT the other day, what a useful set of tools.