How to convert a gff3 to gtf?

Question

[f.fassihian]

Hi all,

I got a gff3 hsa miRNA annotation file from mirBase. I need to convert it to gtf . I tried to do that with cufflinks-2.2.1 on Linux using gffread :

gffread my.gff3 -T -o my.gtf

But my output file is empty! Does anyone have any suggestion how it can be otherwise converted? Any other tools?

Thanks!

Answer 1

[Govardhan Anande]

Hi,

I think this might help you. You can also refer answers here and one script here

Answer 2

[Daniel Standage]

I've been able to find GFF3 to GTF converters (as well as GTF to GFF3 converters) before with some Googling. My go-to is the gt gff3_to_gtf program distributed with GenomeTools.

However, I think it's important to state that any converter between GTF and GFF3 will necessarily be context-dependent. Neither format has a strongly specified schema, only conventions that are used and abused to various different extents throughout the scientific community. What this means is that if you pick two GFF3 files at random from "the wild", chances are they will be structured differently. The differences might be significant, or they might be trivial, but (in my experience) it's almost always enough to trip up a Perl/Python script some scientist scrapped together in a couple of hours.

In my experience, the GenomeTools software is the best in terms of strictly validating GFF3 syntax, but getting a "good" conversion from GFF3 to GTF (or vice versa) often involves some programming.