Question: Extract MAF for whole genome and some species
gravatar for ana16
2.6 years ago by
ana1620 wrote:


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,


galaxy maf uscs • 752 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by ana1620
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
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