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
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