Hello Kaisa,

These are related formats and generally differ only in the 9th column, which is important for data labeling with these tools. The formats as well as some utilities to help with parsing are documented here:
http://cufflinks.cbcb.umd.edu/gff.html
Also note the help email: tophat.cuffli...@gmail.com

For the data files in GFF, you may try contacting the data source and asking for help. It is possible that the attributes needed to create a GTF file exist in other files and the data could be transformed (outside of Galaxy).

Hopefully this helps,

Jen
Galaxy team


On 11/2/11 4:58 AM, Kaisa Thorell wrote:
Hi!

I tried to do as you described but when I come to the tophat/cufflinks analysis 
I can only find .gff files for the strains that I'm working with and no .gtf 
files. What is the difference between them and is there any way to convert the 
.gff into .gtf or does one need any additional information?

Best regards

Kaisa

________________________________________
From: galaxy-user-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Jennifer Jackson 
[j...@bx.psu.edu]
Sent: 28 October 2011 19:42
To: Benoit HENNUY
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] RNAseq Clostridium butyricum

Hello,

The quickest way to use this genome is to load it into your history in
fasta format. Use FTP, as described here:
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

Then, use the "NGS: RNA Analysis" tool set's first step TopHat with the
option "Will you select a reference genome from your history or use a
built-in index?: Use one from the history". Most of Galaxy's mapping
tools have this option, although it may be named slightly differently on
the tool forms.

A double check that your uploaded reference genome has the same exact
identifiers present in any reference annotation GTF file you plan to use
in later steps is a good idea. This will ensure that the TopHat mapping
results will be interpreted correctly by the Cuff* tools. Even minor
differences in chromosome/scaffold names will cause problems and it is
easier to align the naming conventions up-front.

Tutorial and FAQ:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

Best wishes for your project,

Jen
Galaxy team

On 10/28/11 7:38 AM, Benoit HENNUY wrote:
Hi,
I would like to use Galaxy with RNAseq data generated from "Clostridium
butyricum" species. Please, could you include this genome in your list ?
Thank you in advance

Best regards
Benoit HENNUY
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to