Hi Aharon, You can use our Table Browser to generate a list of genes and their locations. Here is a quick guide to get you started:
Click on "Tables" in the blue menu bar at the top of the web page. Select the clade, genome and assembly that you wish to use. For example, if you would like to use the default human assembly (currently hg18) make the following selections: clade: Mammal; genome: Human; assembly: Mar. 2006. For "group" choose "Genes and Gene Prediction Tracks." Then choose the gene prediction track you would like to use (for example: UCSC Genes, RefSeq Genes, etc.). Whichever track you choose, the table that automatically populates will be the primary table for that track and is the table you should start with. You can click "describe table schema" to be sure the selected table contains the information you are interested in. Make these additional selections: region: genome; output format: selected fields from primary and related tables. Click "get output". You will be prompted to select the fields you want displayed before your results are provided. Since you want a list of genes and their coordinates, I would suggest that you choose at least the following fields: name, chrom, txStart, txEnd. Click "get output" to see your results. For more information about using the Table Browser see "Using the Table Browser" by scrolling down past the Table Browser form. It provides brief descriptions of the Table Browser controls. You can also see the "User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. One of our developers also suggested these two additional methods to get this information: If you have the mysql command available on your system, you can fetch gene information with this mysql operation: $ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \ -e "select chrom,txStart,txEnd,name,strand from knownGene;" hg18 Or, from the file dump for this database table: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz I hope this is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Aharon Brodie wrote: > Hi, > Is it possible to create a list of all genes and the start-end locations of > each one? > Thanks in advance, > -Aharon > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
