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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