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.cufflinks@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-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Jennifer Jackson [jen@bx.psu.edu] Sent: 28 October 2011 19:42 To: Benoit HENNUY Cc: galaxy-user@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:
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-- 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:
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