Question: Liftover on galaxy non-functional
gravatar for jstore5
16 months ago by
jstore50 wrote:

I'm attempting to use the liftover function on, 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
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by jstore50
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 (, 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:

Meanwhile, if your UCSC genome is not available/indexed for this tool (yet), you can use the Batch Coordinate Conversion utility directly at 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 COMMENTlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson25k
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