Hi Katrina Thanks for a detailed reply. I got what I wanted.
You guys are super awesome at UCSC browser team. I understand the patience it takes to reply to some of the same repeated questions. Many Thanks! -Abhi -----Original Message----- From: Katrina Learned [mailto:[email protected]] Sent: Thursday, February 25, 2010 1:24 PM To: Pratap, Abhishek Cc: [email protected] Subject: Re: [Genome] Looking for hg18 exons dataset Hi Abhishek, The gene prediction tracks (e.g. UCSC Genes, RefSeq Genes, Ensembl Genes etc.) have the exon start and end positions (exonStarts and exonEnds). In the Table Browser make the following selections: clade: Mammal genome: Human assembly: Mar. 2006 (NCBI36/hg18) group: Genes and Gene Prediction Tracks track: choose the gene prediction track you would like to use table: the default table will be the primary table for that track and is the table you should start with; click "describe table schema" to view descriptions of the table columns. region: genome output format: BED - browser extensible data output file: if you would rather have the results saved to a file instead of displaying in the browser window, enter the name you would like the output file to have, otherwise, leave blank file type returned: plain text Click "get output". Then, select either "Exons plus [0] bases at each end" (will include the 5' and 3' UTRs) or "Coding Exons" (no UTRs), whichever is applicable, and click "get BED. 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. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Pratap, Abhishek wrote, On 2/24/2010 1:42 PM: > Hi All > > I am looking to grab the hg18 based human exon set basically start and end > positions and possibly in BED format. I had a look at the table browser but > it doesn't list the exon track. Can you please guide me. > > Thanks! > -Abhi > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
