Hello, You can use the Table browser to do this. The result will be coordinates.
General query path: 1) Table browser: http://genome.ucsc.edu/cgi-bin/hgTables 2) Set clade, genome, assembly, group=Variation and Repeats, track=[SNP track of your choice], table=[default] 3) Make certain that region=genome 4) Upload or paste in the SNP identifiers (for example, if using the track "SNPs 130" from dbSNP, use rs numbers). To see how the data is formatted for any track that you want to use identifiers to pull data from, click on the "paste" button and at the top there are examples. 5) Output results. For such a short list, you can just view in the browser, or you can download (compressed or not). As you know, more than one location per SNP would indicate non-specificity. Be aware of known genomic duplications (such as PAR regions) as they will produce false duplications. These are generally documented on an assembly's gateway page or possibly through the credit's link to the genome source (that will have assembly details). http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#BatchQuery Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Rodney Perry, Ph.D." <[email protected]> wrote: > From: "Rodney Perry, Ph.D." <[email protected]> > To: [email protected] > Sent: Tuesday, January 12, 2010 9:34:22 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] batching > > Is there a way to query a few dozen SNPs at the same time to see if > they > are duplicated or uniquely located in the genome? I can do this > one-at-a -time but it will take a long time. I just want to see if > any > of the SNPs on this list are uniquely mapped or are duplicated > elsewhere > in the genome. I don't even care to obtain the coordinate, just a > yes > or no to either question is all I need. > > > > Thanks, > > Rodney > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
