Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: No maf dataset available, No options available even though I have upload my data
0
gravatar for peiyuchen0306
20 months ago by
peiyuchen0306 • 0
peiyuchen0306 • 0 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 • 497 views
ADD COMMENT • link •
modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by peiyuchen0306 • 0
0
gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 10 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour