GFF3 TO GTF CONVERSION
0
0
Entering edit mode
3 months 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?

GTF GFF file Hydra annotation GFF3 • 599 views
ADD COMMENT
2
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

gffread annt2.gff3.gz -o ./annt2.gtf -T -g ./Genome_index/Hydra_2.0_genome.fa . I used this wih gffread

ADD REPLY
0
Entering edit mode

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).

ADD REPLY
0
Entering edit mode

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)?

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2562 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6