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Question: Basic Genome Loading Question
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gravatar for gkuffel22
3.8 years ago by
gkuffel22 • 170
United States
gkuffel22 • 170 wrote:

Hi everyone,

We are running a local version of galaxy off of our server. What is the best way to load fasta files into my history to use as my reference genome? I've tried to go to UCSC main from the galaxy menu options to upload but I do not see fasta files. I only am able to get BED files. Thank you for your help.

 
ucsc genome ftp galaxy local • 942 views
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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by gkuffel22 • 170
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gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

To use a Custom Reference genome, obtain the fasta version of the genome from UCSC "Downloads" area. Instructions are provided within each directory as a "readme" file.
http://hgdownload.soe.ucsc.edu/downloads.html

Once you have it, make sure your local is configured for FTP, then FTP file to Galaxy. Use the Upload tool to move it from the FTP staging area into a History. 
http://wiki.galaxyproject.org/Admin/Config/UploadviaFTP

The other option is to install the genome directly into your server as a build-in genome and then build indexes. The "Data Manager" tools in the Tool Shed can help with this.
http://usegalaxy.org/toolshed
http://wiki.galaxyproject.org/Admin/DataIntegration

Best, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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