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Question: Extract MAF for whole genome and some species
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gravatar for ana16
2.6 years ago by
ana16 • 20
ana16 • 20 wrote:

Hello,

I am trying to obtain the whole genomes for some species with Galaxy. I have found the very useful example guide "Making whole genome alignments usable for biologists", published by dan, but it only mentions how to get genomic regions of interest, usually genes. In my case, I would like to analyze the genome of several species. I tried using "Extract MAF blocks" but I am unable to specify the whole genome. Is there a way to access to this data directly from Galaxy?

Thank you in advance,

Ana.
galaxy maf uscs • 752 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by ana16 • 20
1
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you want to work with an entire MAF dataset, then it can be imported from the source and used. UCSC is one choice: these data are found in the Downloads area under the track Conservation.

If you want the entire genome (fasta format), then UCSC is a choice as well as NCBI and others. Galaxy itself is not a genome data repository.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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