Genome annotation: convert gtf to gff3 file

Question

[shinyjj]

Hi Biostars,

Are there tools to convert gtf file into gff3 file? To my knowledge, gff3 file has more information than the gtf file, so to have the same amount of information, converting from gtf into gff3 is more fair than the other way around.

I know bioinfokit(https://github.com/reneshbedre/bioinfokit) can convert gff3 into gtf, but here, I am looking for a tool that can convert gtf into gff3 file.

Thanks

Answer 1

[LDT]

I have started using agat recently and find it super useful. You can use the following function

agat_convert_sp_gxf2gxf.pl -g test.gtf -o test.gff3

for more info, look at: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gxf2gxf.html Also, the developers of agat are super helpful. Whenever I had an issue, they were always super helpful. They are great

Answer 2

[vague-barracuda-4686]

You can use the gtf_to_gff3 utility of genometools, but AGAT is an excellent option.

Converting GFF to GTF