Hello Gabriel, Use a combination of a Custom track with the Table browser for this type of query
The basic steps would be to: 1) Create a BED file of your coordinates and upload as a custom track. If strand is important (probably is) then use at least a BED6 file (name/score can be made-up values) http://genome.ucsc.edu/goldenPath/help/customTrack.html http://genome.ucsc.edu/cgi-bin/hgCustom 2) Go to Table Browser http://genome.ucsc.edu/cgi-bin/hgTables (see help links in top paragraph). Check to verify that your data appears in the group menu "Custom Tracks". 3) Now, set the group, track, table for the dbSNP track (or whichever SNP track you are interested in - if more than one, do them as separate queries). Click on "describe table schema" to understand contents (top of page), linked tables (middle of page), and details/methods (bottom of page). Go back to query page. 4) Create a filter by clicking the intersection "create" button. Select your custom track as the filter. 5) Leave output as default (all field from selected table), name output file for download, and submit. 6) The default output has the SNP rs numbers, genomic locations, and other attributes. An alternative is to change output format to: "selected fields from primary and related tables" where you can limit the columns of output from the main file and/or add data from linked tables. Coordinates for the SNP table follow our standard 0-based start format. Your coordinates must also be in this format for the intersection to work. http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Also, not all source input SNPs may map according to the track's methods/rules - the track details page lists possible reasons for alternate mapping/non-mapping and exception notations. Good luck and be sure to check out the great examples in both the Custom track and Table browser help if you get stuck. Please write back if anything is unclear, Jennifer Jackson UCSC Genome Bioinformatics Group Gabriel Leiva wrote: > Hello, > > > > I have a list of more then 451 SNPs which I only have the position from > Build 36 but not the name.Is there a way to query for the SNP name for more > then one SNP at the time, so I can do all of them at once (instead of one at > the time)? > > > > Thank you very much, > > > > Gabriel Leiva > > === > Gabriel André Leiva-Torres, M.Sc. > Research Assistant (Dr. Silvia Vidal) > McGill Life Sciences Complex > Bellini Pavilion, Room 356 > 3649 Promenade Sir William Osler > Montreal, QC, H3G 0B1 > > Phone: 514-398-2360 > Fax: 514-398-2603 > [email protected] > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
