Question: No maf dataset available, No options available even though I have upload my data
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gravatar for peiyuchen0306
14 months ago by
peiyuchen03060 wrote:

I have upload my data successfully to galaxy from 'get data > upload file'. however, when I'm going to use my data to do some analysis(convert formats maf to BED) he warned me 'no maf dataset available'. Did someone have the problem before? How to solve it? Sincerly thanks for your help.

galaxy • 356 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson25k • written 14 months ago by peiyuchen03060
0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

If working at http://usegalaxy.org, only a few genomes have native indexes for UCSC MAF (Conservation) data: hg38, hg19, dm3.** The database metadata attribute must be assigned to the other input datasets to access these indexes. How to assign the database to a dataset: https://galaxyproject.org/support/datatypes-and-tools/

If working with another genome, MAF data can be loaded from other sources and used as custom MAF (tool form option: MAF Source > Alignments in Your History).

UCSC is one source -- download locally from UCSC in the genome > conservation track area using their instructions (do not extract from the Table Browser, the data is too large). Then FTP upload to Galaxy. https://galaxyproject.org/ftp-upload/

More details are in several other related posts, see the far right side panel or do a search with the keyword "maf". For example: https://biostar.usegalaxy.org/p/12201/

I created an enhancement ticket that addresses making native index information easier to find. Give it a thumbs up (you or anyone reading this), if you think this would be helpful. Voting on enhancement ideas (and creating them!) helps our team to learn what is important to the community on the usage side of Galaxy design. https://github.com/galaxyproject/galaxy/issues/3915

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 4 months ago • written 14 months ago by Jennifer Hillman Jackson25k
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