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Question: Liftover on galaxy non-functional
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gravatar for jstore5
16 months ago by
jstore5 • 0
jstore5 • 0 wrote:

I'm attempting to use the liftover function on usegalaxy.org, but no matter which file I use, the "To" parameter tells me that there are no options available. Is there any way to fix this problem?

galaxy • 419 views
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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by jstore5 • 0
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gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Make sure the input dataset has the metadata "database" assigned.

The genome mapping indexes for this tool are sourced from UCSC. So, only databases sourced from UCSC will work with the native indexes.

Note that at Galaxy Main (http://usegalaxy.org), not all indexed UCSC databases have liftover indexes. Our data procedures have changed and updating to include all available files is on the short list for new data additions. Follow progress here: https://github.com/galaxyproject/galaxy/issues/1470

Meanwhile, if your UCSC genome is not available/indexed for this tool (yet), you can use the Batch Coordinate Conversion utility directly at http://genome.ucsc.edu. This tool does not have a direct Galaxy import function, but the output can be downloaded from UCSC then uploaded to Galaxy.

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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