Hello, Carsten. Since liftOver maps the start and end coordinates separately, if there has been a rearrangement in one of the species, the size of the region being mapped may change dramatically after mapping. In most cases, this shouldn't happen, but the warning is simply meant to make the user aware of that possibility.
Also, have a look at this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2011-September/027061.html Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Carsten Raabe Sent: Wednesday, December 14, 2011 12:10 AM To: [email protected] Subject: [Genome] lift over 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
