RNAseq Clostridium butyricum

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RNAseq Clostridium butyricum

Benoit HENNUY
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

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Re: RNAseq Clostridium butyricum

Jen Hillman-Jackson
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
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org