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 

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" ?


Jianguang Du
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