Hello, Pierre. You can actually accomplish this using our Table Browser. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
1. From http://genome.ucsc.edu, select "Tables" from the blue navigation bar at the top of the screen. 2. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Region: Select either "genome" for the entire genome or specify a region next to "position" Identifiers: If you already have a list of identifiers you want to convert, you can click "paste list" or "upload list" to enter them. Otherwise, the Table Browser will output every UCSC Gene contained in the region you specified above. Output format: selected fields from primary and related tables 3. Click the "get output" button 4. In the "Select Fields from hg19.knownGene" section, check the "name" checkbox 5. In the "hg19.kgXref fields" section, check the "geneSymbol" checkbox 6. Click the "get output" button Please contact us again at genome@soe.ucsc.edu if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: genome-boun...@soe.ucsc.edu [mailto:genome-boun...@soe.ucsc.edu] On Behalf Of Bushel, Pierre (NIH/NIEHS) [E] Sent: Friday, March 30, 2012 12:07 PM To: 'genome@soe.ucsc.edu' Subject: [Genome] How to convert a UCSC gene name/alignID to a gene symbol gene name How do I use R and possibly the BSgenome Bioconductor package to convert a UCSC gene name/alignID such as uc001bvd.3 to a gene symbol and gene name/description such as MARCKSL1 and Homo sapiens MARCKS-like 1 (MARCKSL1), mRNA? _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
