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.
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