Hello Avi, If you type in the command at the prompt, a list of options will appear along with usage. The over.chain files are in Downloads, ftp directory goldenPath/<from_species>/liftOver/.
For default genomic examples, there are two classes: same species lifts and cross-species lifts. Both can be seen in the web version [UCSC Browser home page -> Utilities -> Batch Coordinate Conversion (liftOver)] http://genome.ucsc.edu/cgi-bin/hgLiftOver The most basic option for genomic would be to set -minmatch = 0.95 for same-species and = 0.1 for cross-species and leave the rest as default. For any failures, you can examine the reasons and play around with the parameters, such as setting multiple = Y. But beware that this can produce significant output if minmatch is low and chain and hit size are set >= 0. It will probably take a few attempts to tune these in various combinations so that the output is useful for your particular needs. The other options come into play for gene, transcripts and other annotation types that are lifted. Again, the program runs pretty fast even on large datasets, so a cyclic test-and-analyze approach is probably the best way to find your own best parameters to create useful lifted data. FAQ in case you have not seen it: http://genome.ucsc.edu/FAQ/FAQdownloads#download28 Good luck and please write back if you need more technical help, Jennifer Jackson UCSC Genome Bioinformatics Group Fungazid wrote: > hello genome browser staff, > > I would like to map species A genomic coordinates to species B genomic > coordinates (e.g. mouse -> human). To my knowledge liftover can do it (I also > tried to workaround by blating the query region with gfserver/gfclient, but > this is too slow for large tables). I have Liftover installed on Linux, but I > didn't find any documentation about input parameters and examples. > Maybe you can help, or direct me to a proper documentation. > > > Thanks, (also you for your previous help) > Avi > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
