Hello Yanming,

To set-up native NGS data indexes, please see the instructions in this wiki:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

Uploading data into a history in fasta format will allow that dataset to be used as a custom reference genome with most tools, which is another option. This wiki explains how the Custom genome method works:
http://wiki.g2.bx.psu.edu/Learn/CustomGenomes

Hopefully this helps!

Best,

Jen
Galaxy team

On 3/23/12 11:06 AM, Yang, Yanming wrote:
Hi,

I have just installed a Galaxy instance at my local machine and uploaded some 
sequence data into it. But, when I tried to use some NGS tools which need 
reference genome, I found the selection window was empty. I wonder how to get a 
reference genome data (e.g., hg19) incorporated into the local Galaxy.

Any help will be greatly appreciated. Thanks!

Yanming Yang


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