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Question: How can I switch 46-way multiZ in stich MAF blocks of galaxy?
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gravatar for wlnjseu
3.0 years ago by
wlnjseu • 0
United States
wlnjseu • 0 wrote:

 

Because I need to use phyloCSF, I uploaded a bed file of zebrafish and want to get a multiple alingment of 29 mammalian genomes. 3 months ago, I  used 46-way multiZ in stich MAF blocks, but now only 100-way multi.

I saw the post of "How can I switch 46-way multiZ(hg18) in stich MAF blocks of galaxy?", but I have not resolved my question.
galaxy • 828 views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by wlnjseu • 0

Hello - I see the prior post and this question but am not quite sure what you are asking help for. Could you explain in a bit more detail? Thanks! Jen, Galaxy team

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for wlnjseu
3.0 years ago by
wlnjseu • 0
United States
wlnjseu • 0 wrote:

I want to get a multiple alingment of 29 mammalian genomes in stich MAF blocks. I can find 46-way multiZ in stich MAF blocks 3 months ago, and the 29 mammalian genomes were included in 46-way multiz in stich MAF blocks. However, there is only 100-way multiZ in stich MAF blocks at now, no 46-way multiz. The 29 mammalian genomes were partly included in 100-way multiZ. How I can select 46-way multiz in stich MAF blocks. Thanks!
ADD COMMENT • link written 3.0 years ago by wlnjseu • 0
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Thanks for explaining. UCSC's hg19 46-way Conservation track was replaced with the updated 100-way track. If you want to use alternate MAF data with these tools, the data can be loaded into a history and used that way. Or you can start up a personal local or cloud Galaxy and install the data natively there for use. 

If you need help doing any of this, let us know what option you want to try and we can share more details.

Thanks, Jen, Galaxy team

 

 

 
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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