Hello Richard, Unfortunately we cannot provide lifts between species we do not display in the browser let alone strains. The process we use to generate the liftover files is somewhat involved and an easier solution would be to simply BLAT the regions you are looking to map. It sounds like you have quite a few regions - in which case we recommend downloading and using our standalone BLAT utility. You can read more about that in this FAQ:
http://genome.ucsc.edu/FAQ/FAQblat.html#blat3 Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 06/01/11 05:03, Richard Badge wrote: > Dear genome browser mailing list, > > I came to send this email at the suggestion found on this page > (http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert) that if an > over.chain file does not exist for a given pair of species that you may be > able to generate one for us... > > My colleagues and I are engaged in mapping SNPs between two yeast strains > (Y55 and SK1) that have partially completed reference genome sequences. We > would like to be able to ascertain the coordinates of corresponding SNP > positions between the two genomes, as part of a recombination breakpoint > mapping project involving genome re-sequencing of meiotic tetrads. > > We were aware of the utility of liftover in moving annotation from one > assembly to another, and wondered if it could similarly be used for different > strains (these are estimated to be about 0.5% diverged at the nucleotide > level). Ultimately the over.chain file will give us a means to equate SNP > positions, and to validate our sequence read mappings... > > If this is a possibility, or you could let us know how such a file can be > generated, we would be very grateful, > > Regards > > Richard > Dr Richard Badge, Lecturer > Department of Genetics, > Office 130, Adrian Building, > University of Leicester, > University Road, > Leicester > LE1 7RH > Tel (Office): 0116 2525042 > Tel (Lab): 0116 2523416 > Fax: 0116 2523378 > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
