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Question: Adding mm10 genome to Amazon Cloud Instance
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gravatar for jdelmarmol
4.4 years ago by
jdelmarmol • 0
United States
jdelmarmol • 0 wrote:

Hello, 

I am trying to upload my RNA seq data to analyze using Amazon Cloud and I can't find the latest version of the mouse genome (mm10) as a genome option. I found that I could download it from the genome browser (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/) and then upload it myself to Galaxy, but I find it only in .2bit format, from which I would have to convert into fasta format and then upload. It just seems strange and I am wondering if I am doing something wrong.

I appreciate any help!

Thank you,

Jo

 
galaxy • 1.1k views
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by jdelmarmol • 0
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gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello Jo,

This is one way to do it - UCSC does not always provide the .fasta, but Galaxy currently requires both the .fasta and .2bit for full functionality with most commonly used tools, so it is worth installing both.

If you want to see our configuration, and perhaps copy it, it is available via rsync (along with all other reference genomes/indexes hosted on the public Main Galaxy instance). Using Data Managers is also an option. The links below cover these methods.
http://wiki.galaxyproject.org/Admin/DataIntegration
http://wiki.galaxyproject.org/Admin/UseGalaxyRsync

Regards, Jen, Galaxy team
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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