Question: Convert .gbff (gene bank flat format) to gff3, gtf
0
gravatar for alex
6 months ago by
alex0
alex0 wrote:

As an example, I'm working with a reference genome for pineapple and need a GTF and GFF file. This is the assembly ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/162/155/GCA_902162155.2_F153.v0709/

All that's available is a .gbff file. I'm looking for a way to convert this into a gff3 and gtf file.

I am able to convert the gbff into a gff3 using bp_genbank2gff3

Using genome tools, I can validate this gff3 by running

gt gff3validator my.gff

and it tells me it's valid. But when i try and convert this gff to a gtf using either genome tools

(gt gff3_to_gtf my.gff)

or gffread

(gffread my.gff3 -T -o my.gtf)

it generates an empty file.

Am i going about the the right way?
Any help is appreciated

gbff genebank gff gtf genome • 800 views
ADD COMMENTlink modified 6 months ago by Juke345.2k • written 6 months ago by alex0

If you are able to use a different assembly then there is a GFF file available.

ADD REPLYlink written 6 months ago by GenoMax96k
2
gravatar for Juke34
6 months ago by
Juke345.2k
Sweden
Juke345.2k wrote:

It is not annotated, there is no gene model in the gbff file.

ADD COMMENTlink written 6 months ago by Juke345.2k

So essentially this is not possible? Is there any other way to generate a gtf in this case?

ADD REPLYlink written 6 months ago by alex0
1

You can perform your own annotation, but it can be quite tough

ADD REPLYlink written 6 months ago by Juke345.2k

Understood. Thank you very much for your answer!

ADD REPLYlink written 6 months ago by alex0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1004 users visited in the last hour
_