Hello,

The option is "Use a built-in index" to use the mm9 reference genome database already in Galaxy (most likely what you want to do).


Thanks,

Jen
Galaxy team

On 8/14/12 8:31 AM, Du, Jianguang wrote:
Dear All,

I am going to run Tophat with mouse RNA-seq datasets. When I uploaded
the datasets with URL method, I chose "Mouse July 2007 (NCBI37/mm9)
(mm9)" under *Genome*. So " database: mm9" appears in the brief
description of each dataset in history.

My question is: when I run Tophat, under "Will you select a reference
genome from your history or use a built-in index?", should I selct "Use
a built-in index" or "Use one from the history" ?

Thanks.

Jianguang Du



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