Hello Dick, You can use the Table browser for this query.
The general idea would be to: 1) set the clade/genome/assembly for hg19 (GRCh37) 2) set group=Genes and Gene Prediction Tracks 3) set track=UCSC Genes and leave default table=knownGene 4) set region=genome 5) upload your identifiers 6) output format: selected fields from primary and related tables 7) name file and "get output" 8) on next form, select desired output fields from knownGene and kgXref as desired. You may also want to add in the kgAlias table and select fields from that table, too, since that is the table your original gene names were compared against (it will make it easier to find transcript's pulled by a particular identifier you entered). Output may have multiple rows per initial query gene symbol. You will have to do some analysis to determine which variants to retain/use. Linking in other tables can help: knownIsoforms - clusters knownGene transcripts into "genes" - not necessarily the same way that gene symbol has been assigned by other processes knownCanonical - is the selected "representative" transcript per clustered "gene". briefly, this is the longest, most complete, most 5' transcript (see track description). This may or may not be what you consider to be the best "representative", but it may be a place to start. Help/FAQs: Table browser: http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#BatchQuery If you find the query to be slow, try using less identifiers per query cycle. This should help to get you started. Please let us know if you have any questions as you move through the analysis, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/11/10 8:02 AM, [email protected] wrote: > Hi, > I have a list of 11,015 gene symbols that I would like to associate > genomic build 37 locations with. Can you tell me how to do it? > > This is for building and array CGH. > > Thanks very much, > /Dick > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
