Genome annotation file GFF3 and GTF same? interchangeable?

Question

[SKY]

GFF3 contains annotations for Non-coding RNA and GTF doesn't. Is it? Can GFF3 be used as a re-placement of GTF for StringTie?

Please help me clear this doubt...

Thanks Akash

Answer 1

[boczniak767]

These two files contain similar information - feature annotation.

But there are important differences, take a look at specification at the UCSC.

Generally gtf is more standardised than gff.

[Juke34]

I don't get why they still talk about GFF1 as it was an up to date format at UCSC while this format has been abandoned since 2 decades now... Do they really still use it?

Answer 2

[Juke34]

Actually GTF can contain ncRNA, the 3rd column will be described as transcript and an extra attribute in the 9th column will say that it is of type ncRNA. It really depends from where you catch your file. GTF and GFF do not have the same syntax so if they ask for GTF and you want to feed the tool with your GFF you have probalby first convert your GFF file into GTF (see agat_convert_sp_gff2gtf.pl in AGAT). And vice et versa.

see here for more information about the GFF/GTF format: https://agat.readthedocs.io/en/latest/gxf.html

[SKY]

Thank you for the explanation. However, my tool 'StringTie' can recognize both GTF and GFF3 so conversion isn't required i guess. reference: see -G option here, https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual