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
