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