Hello YU, Use the Table Browser and the UCSC Genes track.
I was able to produce this table (header line shows the data source table.field): #hg19.knownGene.name hg19.knownGene.chrom hg19.knownGene.strand hg19.knownGene.txStart hg19.knownGene.txEnd hg19.kgXref.geneSymbol hg19.knownToLocusLink.value uc002yvg.2 chr21 + 37536838 37666571 DOPEY2 9980 uc002yvh.2 chr21 + 37617345 37634208 DOPEY2 9980 uc011aeb.1 chr21 + 37537005 37666571 DOPEY2 9980 Query path: 1) start with hg19 and the UCSC Genes track 2) paste in the list of gene names (or another identifier present in the kgAlias table). for the example, I used DOPEY2. Or, leave empty for all data. 3) select output type "selected field from primary and related tables" 4) name file for output and click on "get output" 5) on the next form, add in tables then check the fields you want for download. You can use the same table.fields as I did (above) or customize as desired. Note: knownGene and kgXref will be selected by default. knownGene will have the genome mapping information, so check boxes for that data. You shouldn't need anything from kgXref, so uncheck all of that table's boxes. 6) click on "get output" again, this time under the first table (knownGene). file should download. Help for Table browser: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SelectedFields Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/25/10 11:37 PM, Yuan Jian wrote: > hello UCSC genome browser team, > > could you tell me how to download a table including Entriz geneID and loci. > something likes > > geneSymbol geneID chr start end strand > DOPEY2 9980 chr21 37536839 37666572 + > ... > > YU > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
