Hello Yan, Help for using a Custom reference genome is on this wiki and the links it points to: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Hopefully this helps, Jen Galaxy team On 8/6/12 9:10 PM, Yan He wrote:

Hi everyone,

I am wondering if I can use user-defined reference instead of selecting the reference genome listed in Galaxy while doing mapping. If we can, how can I choose the uploaded reference instead of selecting the reference genome? Any ideas are greatly appreciated!

Cheers,

Yan

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