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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___________________________________________________________
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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