18 months ago by
Data from this tool is only available from UCSC and is based on the UCSC-sourced genome builds. The tool interprets the dataset assigned "database" metadata for the input BED/GTF and presents mapping options when available.
If the data are not assigned to the UCSC version of the build, then no liftOver data will be available in the tool. The underlying mapping data is generated by UCSC as part of their "Conservation" track. It is the only stable source of the data publicly available that I know of.
In addition, not all UCSC genome builds have this information available and/or there is available data but it has not been added to Galaxy at http://usegalaxy.org (yet). I am not sure what genome you are using, but
hg19 to hg38 and
mm9 to mm10 are both available (and the reverse).
Data that is not based on the UCSC-version of the genome build cannot just be assigned to a UCSC database. The identifiers need to be modified first (when that is even possible), otherwise, the liftOver tool will error. More about genomes and chromosome identifiers. https://galaxyproject.org/support/chrom-identifiers/
Thanks! Jen, Galaxy team