Hello Richard, Thank you for your question. In order to receive a more timely answer and for the benefit of all of our users, for whom we try to have the most comprehensive archives, I would appreciate it if you resent your email to [email protected]. Thank you for your understanding in this matter.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 6/7/11 2:09 PM, Richard Badge wrote: > Hi Pauline, > > I wonder you could clarify what "somewhat involved" is. > > I can see how using blat to align the sequences would be feasible, but we > would still need to parse the alignment to achieve equivalencing between base > positions in the two strains. > > I was assuming that the over.chain file, once generated, could be used as a > substrate for the liftover utility, along with our list of SNPs to convert > coordinates between the two. As we have 24 complete genomes worth of SNPs, > manually or even scripted individual alignments would seem an inefficient > approach... > > Any light that you could shed would be greatly appreciated, > > Regards > > Richard > On 3 Jun 2011, at 02:11, Pauline Fujita wrote: > > >> 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 >>> > > Dr Richard Badge, Lecturer > Department of Genetics, > University of Leicester, > Leicester > LE1 7RH > Tel: 0116 2525042 > > Dr Richard Badge, Lecturer Department of Genetics, University of Leicester, Leicester LE1 7RH Tel: 0116 2525042 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
