Combine different functional annotations

Question

[ahmadjoyyia]

Hi, I have performed functional annotation of complete genome using number of available databases like BlastP, KAAS, TRAPID and a few others. I want to combine all these functional annotations in final_EVM.gff3. How can I do it? If you can share any tutorial, paper or your experience!

Thanks in advance.

[Juke34]

For BlastP result you can probably use agat_sp_manage_functional_annotation.pl, for the others you can use a tabulated format and use agat_sq_add_attributes_from_tsv.pl from AGAT.

[ahmadjoyyia]

Thanks but Mercator actually gives output in .fa How will I combine it? And I have also performed Swissprot blast as well. I am pretty confused. What is the standard practice by the way? Or everyone has their own way of doing it?

[Juke34]

Right AGAT use only gff/gtf format, you would need to nap back to the référence genome to get these formats.