Hello, The quickest way to use a genome that is not already indexed is to load it into you history and select it as a custom genome from the TopHat tool form with the option: "Will you select a reference genome from your history or use a built-in index?:" -> "Use one from the history" Instructions are included in this wiki: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes This genome is sourced from UCSC and is available here: http://hgdownload.cse.ucsc.edu/downloads.html Best, Jen Galaxy team On 3/21/12 2:07 PM, Evgeny Brud wrote:

Hi, Could galaxy include the Drosophila yakuba reference genome for use with Tophat? It's not listed. ___________________________________________________________ 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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