dear all, I am writing to you because I am not clear about the following statements about the liftOver utility: The important sentences in bold
The LiftOver <http://genome.ucsc.edu/cgi-bin/hgLiftOver> tool, accessed via the Utilities link on the Genome Browser home page, also supports forward, reverse, *and cross-species conversions, as well as batch conversions. * If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool. *The executable file for this utility can be downloaded here <http://hgdownload.cse.ucsc.edu/admin/exe/>. LiftOver requires a UCSC-generated /over.chain/ file as input.* Pre-generated files are available for selected assemblies from the Downloads <http://hgdownload.cse.ucsc.edu/downloads.html#liftover> page. If the desired file is not available, send a request to the genome mailing list <http://genome.ucsc.edu/contacts.html> and we may be able to provide you with one. Here is what I did: I downloaded the executable for the utility and the corresponding lift over chain file (*>>>* mm9 to hg19) and executed the script, however I am confused by the following hint within the man pages of the lift over utility : *********************************************************************** *WARNING: liftOver was only designed to work between different assemblies of the same organism, it may not do what you want if you are lifting between different organisms.* *********************************************************************** therefore can I convert coordinates cross species or not ? cheers and as usual thanks in advance. Carsten _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
