Hello, Miriam. You can do this by 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.
You will need to choose a gene prediction track to use for your query. To read more about each gene prediction track, you can consult the description pages for each. To see the description for any track, you can click on the gray bar to the left of the track in the main display or click on the track title above its configuration pulldown menu (i.e. for UCSC genes http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene). Let's assume for this example that you're interested in genes from the human RefSeq Genes track. Perform the following steps: 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: RefSeq Genes Table: refGene Region: If you're just interested in one region, enter it in the box to the right of "position". If you're interested in several different locations, click the "define regions" button. You can either paste a list of coordinates or upload a file containing the coordinates. When done, click the "submit" button. Output format: Selecting "all fields from selected table" will output everything from the table. If you select "selected fields from primary and related tables," you can select which fields you would like to include in your results. For the refSeq track, you will want to include the "name" or "name2" columns which are the gene name(s). To see a description of the fields for a given table, you can click on the "describe table schema" button in the Table Browser. 3. Click the "get output" button. 4. If you selected "all fields from selected table," your results will be displayed. If you selected "selected fields from primary and related tables," you can check the fields you are interested in. Once you are done checking fields, click the "get output" button. You can experiment to see which options work best with your needs. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Miriam Ragle Aure Sent: Wednesday, January 18, 2012 8:25 AM To: [email protected] Subject: [Genome] Converting genomic positions to gene names? Hi, Do you know if it is possible to convert a list of genomic positions (chromosome, position) to the corresponding gene name of this locus? Thanks! Best regards, Miriam _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
