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Question: Concatenate locally cached assembly
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gravatar for tbg5023
8 months ago by
tbg5023 • 0
tbg5023 • 0 wrote:

I wish to create a custom build of the mm9 assembly by inserting a FASTA file. Is there a way I can use the concatenate tool with the locally cached mm9 to create a new custom genome?
build genome concatenate source custom • 260 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by tbg5023 • 0
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, you can modify nearly any fasta files to create a custom genome/build. For your case, both source fasta files must be loaded into your history first. Make sure the formatting is exactly the same with NormalizeFasta before using Concatenate.

The source for the locally cashed mm9 genome is UCSC (Downloads area, http://genome.ucsc.edu). Download locally from UCSC, then upload to Galaxy using FTP.

FAQ: https://galaxyproject.org/support/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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