Hello, Wayne. It sounds like what you're suggesting can be accomplished by using the Table Browser. If you aren't familiar with the Table Browser, you can view the OpenHelix browser tutorial at http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml or the Table Browser User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
First, you'll need to know which track contains the data you're interested in. All of the gene tracks are listed under "Genes and Gene Prediction Tracks." Clicking the link on any track will take you to the track description page. Near the top of this page, you will find the date the data was last updated. If you click on the "UCSC Genes" page, you will find that it was last updated on 08-Oct-2009. The "RefSeq Genes" page shows that the data was last updated on 20-Oct-2011. You want to be sure you're working with the most recent set of data. Clicking "Tables" in the blue navigation bar at the top of the screen will take you to the Table Browser. Let's assume you want to work with the human (hg19) RefSeq Genes track. You would select the following: clade: Mammal genome: Human assembly: Feb. 2009 (GRCh37/hg19) group: Genes and Gene Prediction Tracks track: RefSeq Genes table: refGene output format: all fields from selected table If you're not certain what data is available in a specific table, you can click the "describe table schema" button which will show the fields in that table and give an example of the type of data that exists in those fields. Note also that you can set "region" and "identifiers" to query the entire genome or only a specific position or specific identifiers that you specify. Click the "get output" button which will give you all of the information from your table. If you don't want ALL of the information in the table, but you only want SOME of it, you can change "output format" to "selected fields from primary and related tables." For example, if all you wanted to display was the chromosome, exon start and stop positions and transcript id, you would click the "get output" button and then check: name chrom exonStarts exonEnds name2 Then click the "get output" button. Only the information you checked is displayed in the results. Notice that below the primary table is another table called "Linked Tables." If you wanted to include related data from other tables, you can check the specific table you're interested in and then click "Allow Selection From Checked Tables." The fields from your selected tables will then be visible and you can check whichever additional fields you want to be included in your output. You can experiment to find the set of options that best displays the information you are interested in. 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 Wenyue Sun Sent: Thursday, October 27, 2011 8:33 AM To: [email protected] Subject: [Genome] Gene Exon Start End Position Transcript Dear Help Desk, I am writing regarding download the exon information for a batch of Genes (Most Updated). Specifically the information could include exon start position and end posision along chromosome and their transcript id. Could you let me know a way that we could handle? Thank you. Sincerely, Wayne _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
