Hello Wigdan, Do you have the rsIDs for the SNPs from Build 35? If so, you can use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to retrieve the corresponding Build 36 coordinates.
In the Table Browser, select Build 36 (Mar. 2006), and the SNPs (129) track. Make sure "region: genome" is selected, then hit the "filter: create" button. On the next page, paste the entire list of SNPs (rsIDs) in the "name does match" box, then hit "submit". Choose "output format: selected fields from primary and related tables" and hit "get output". Select the boxes for chrom, chromStart, chromEnd and name and hit "get output" again. You should get a list of all of your SNPs of interest, along with their positions in Build 36 coordinates. I hope this is helpful. If you have further questions, please feel free to write back to [EMAIL PROTECTED] -- Brooke Rhead UCSC Genome Bioinformatics Group Wigdan Al-Sukhni wrote on 11/27/08 10:46 AM: > I have a set of genomic regions with the Build 35 coordinates as well > as the start and end SNP markers that correspond to those regions. Is > there a way to obtain the equivalent Build 36 coordinates for those > regions using the SNP markers (rather than using Liftover with the > Build 35 coordinates)? I know that I can plug in the start and end > SNPs for each region individually into the browser and get the > corresponding Build36 region; however, I need to do so for a large > number of regions, is there such an option to do them all at once? I > am avoiding Liftover because I get a significant failure rate. > > Thanks, > Wigdan Al-Sukhni, MD > University of Toronto > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
