Entering edit mode
2.3 years ago
Shagnik
•
0
Hi,
I am trying to convert the Hydra2.0 augustus gene models available in gff3 format in Hydra2.0 Web portal. I want to get the GTF file?
Can anyone help me out with this conversion as I am repeatedly failing. I have tried gffread, agat and genometools. Maybe the coding needs some correction.
Or can I get the corresponding GTF file directly on the web somewhere?
Good morning !
Can you show us some examples of what you have tried with the tools you mention ?
It will help us to correct your code if needed ! For this type of conversion, I use gffread as well and it works very well.
gffread annt2.gff3.gz -o ./annt2.gtf -T -g ./Genome_index/Hydra_2.0_genome.fa . I used this wih gffread
I agree with Rox, gff3 to GTF should work with gffread. Alternatively, the Hydra2.0 augustus gene model in GTF format can be downloaded on the dryad website (click "download dataset"). However, it will also download a bunch of other stuff you probably don't need (according to this github page).
try https://github.com/reneshbedre/bioinfokit and tutorial: https://www.reneshbedre.com/blog/gffgtf.html.
I would be vey interested to know the type of failure you get with AGAT. If you fail with all these tools I guess it is more a structure problem... i.e. do you have 9 columns? is it tab delimited? do you have proper carriage return at the end of lines (you can try a dos2unix command)?
There was a package published recently for this purpose. I expect it will be able to make the conversion that you need. https://gfacs.readthedocs.io/en/latest/Getting_Started/Formats.html