Create GTF or GFF3 file from draft genome

[bernardo_bello]

Hello Bioinformatic community,
I recently entered in RNA-Seq world, I’m a second year PhD.
We have recently sequenced a bacterial transcriptome. I would like to create the GTF or GFF3 file from the bacterial genome in order to add it to Cufflinks. The draft genome is still unpublished. We have run the PGAAP http://www.ncbi.nlm.nih.gov/genomes/.../Pipeline.html pipeline to annotate it, but PGAAP do not gives GTF or GFF3 file. Instead, PGAAP gives you GenBank File. If someone could advise me how to do it I will be very grateful. Maybe Artemis can do it.

Last, say that I'm a biologist, so I need GUI to work, no programming experience, sorry.

Thank you very much, Bernardo

[scottyler89]

creating a GTF file

I'm in basically the same situation, but I'm teaching myself the programming. Unfortunatly I don't think there is a program with a real GUI, except perhaps the GALAXY sites.

http://galaxyproject.org/

On the public (Penn State) run site, I think there is a 2 Gig max, which would likely be preventative for both importing a genome, and transcriptome, but depending on the formats you have them it, it might be possible. You will want to use cufflinks to make the GTF file, unless anyone else knows of another program.

http://cufflinks.cbcb.umd.edu/manual.html#cufflinks_output

Galaxy has simplified it to a 'type into the text boxes' and click go type of format. Otherwise, I think you will likely have to start using linux, like I have. It can be a pain, but it's well worth it.

[bernardo_bello]

Hi scottyler89:

>I'm in basically the same situation, but I'm teaching myself the programming. Unfortunatly I don't think there is a program with a real GUI, except perhaps the GALAXY sites. http://galaxyproject.org/

I found this tool and it helps:

http://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

>I think you will likely have to start using linux, like I have. It can be a pain, but it's well worth it.

I really would like to have time to learn linux. I would start by install/unistall programs and trying to run them. Many command-line tools are now adopting GUI for biologists.

Bests regards,

Bernardo

[scottyler89]

wow - very nice! I've bookmarked that site for later. I'm sure it will come in handy. Thanks!

Best wishes,
Scott