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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