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Question: Is there an mm10 MAF?
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gravatar for dvanic
4.0 years ago by
dvanic • 0
Australia
dvanic • 0 wrote:

Is there an mm10 MAF that can be used? Or is Galaxy only supporting hg19?

Thanks in advance!
history tools datasets maf • 789 views
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modified 4.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by dvanic • 0

I have the same question. Thanks!

ADD REPLY • link written 12 months ago by Elliott • 0
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gravatar for Jennifer Hillman Jackson
4.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Any MAF can be used in Galaxy with the tools, but only a few are included as build-it reference data on the public Main Galaxy instance at http://usegalaxy.org. These do not include mm10 at this time.

If you are working on a local/cloud Galaxy, a MAF dataset can be installed as a build-in reference file. See our admin instructions and model after the currently included MAFs from the rsync server. Or, if just want to use it on a public site, load it into your history and use it from there. 
http://wiki.galaxyproject.org/BigPicture/Choices
http://galaxyproject.org (Admin)

The mm10 MAF at UCSC is a good choice: http://genome.ucsc.edu/ --> review track in mm10 browser ("Conservation") and obtain the files from their downloads area.

Adding this to Main is worth considering. I'll follow up on this and create a ticket/post it back if a yes.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k
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