Merge braker.gtf and SQANT3.gff3 file

Question

[anna_shin]

I have some question with merging braker.gtf and SQANTI3.gff3 file.

First, I generated BRAKER.gtf file with my new genome assembly,

and then, I generated isoform.gtf file using "flair program" with BRAKER.gtf and Long read RNA-Seq data.

Finally, I generated final gff3 file using SQANTI3 file.

I want to merge "BRAKER.gtf" file and "SQANT3.gff3" file in order to generate final total annotation gtf file. is there any way to do this process???

thank you.

[GenoMax]

AGAT toolkit generally is useful with all things related to GTF/GFF. Check it out here: https://agat.readthedocs.io/en/latest/agat_for_you.html

[anna_shin]

thank you. I will try using AGAT toolkit.