Hi Stefan, I would suggest uploading your SNP list as a custom track and using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to intersect it with the ensGene (Ensembl) table for bosTau3 (3.1). These previous mailing list questions should explain how this can be done:
https://lists.soe.ucsc.edu/pipermail/genome/2006-December/012343.html https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013638.html https://lists.soe.ucsc.edu/pipermail/genome/2008-February/015641.html Please let us know if you have any additional questions or need additional help: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 8/29/11 12:40 AM, Stefan McKinnon Høj-Edwards wrote: > Dear mailing list, > > I hope this is the right forum to ask my question: > I have a large set of snp-markers, which are mapped to the UMD3.1 bovine > genome assembly. My quest is to map these markers to genes. I have succeeded > doing so with the ensemble genes, but these are mapped to the Btau4.0 genome > assembly. > The question is now, is there a large difference between the assemblies; that > is, can I use the genes mapped to Btau4.0 assembly? > If not, where can I find a table of genes (and their location) mapped to > UMD3.1? > > For reference, I have found the ftp-site for the UMD3.1, but all genes I can > see are "Derived by automated computational analysis...". > > Thank you in advance, > > Stefan McKinnon Høj-Edwards Dept. of Genetics and Biotechnology > PhD student Faculty of Agricultural Sciences > [email protected] Aarhus University > Tel.: +45 8999 1291 Blichers Allé 20, Postboks 50 > Web: www.iysik.com DK-8830 Tjele > Tel.: +45 8999 1900 > Web: www.agrsci.au.dk > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
