Hi, I wanted to covert mm10 coordinates to susScr11 using the LiftOver tool, but the latest assembly of the pig genome (susScr11) does not appear in the list of genomes mm10 can convert to. Would it be possible to add that assembly to the tool? Or would there be any other way I could convert my coordinates ? Best regards and thanks !
Yes, most of the recent UCSC genomes have not been indexed for this tool yet. We are working on a project to add more indexes and sync those across all usegalaxy mirror servers. More genomes/data will be added then, including all of the liftOver indexes from UCSC.
Meanwhile, use the Batch Coordinate Conversion Utility at UCSC directly: https://genome.ucsc.edu. Those results can be uploaded to Galaxy after to work with them.
Thanks! Jen, Galaxy team