On Mon, Nov 30, 2009 at 12:22 PM, Jennifer Jackson <[email protected]> wrote: > Hello, > > There are a few choices: ftp files from Downloads, extract file (table) using > the Table browser, or output the file (table) using the public mySQL server. > > For most gene tracks, the primary table is in genePred format. This includes > the coordinates of exons and notes the utr and cds regions. > http://genome.ucsc.edu/FAQ/FAQformat#format9 > > Downloads: > The name of a table in the database is the same as a file on the Downloads > server (with an added .txt.gz for the data and an added .sql for the mySQL > schema. All database files on the Downloads server are located by following > the links Downloads -> common name -> genomic assembly version -> annotation > database directory. http://genome.ucsc.edu/FAQ/FAQdownloads#download1
I'm on the following page. There are many files. Which file I should download to get the exon region information? http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/ > Table browser: > Probably the best option. Open the tool, set the controls to the mouse > assembly of interest, then track group "Gene and Gene Predictions" and then > the gene track of interest (UCSC Genes or RefSeq or another of your choice). > Then, leaving the primary table (the genePred table) selected, click on the > view schema button. The page has three sections - the table/file schema, a > list of associated tables along with the linking keys, and sample data or the > track description (same description found by clicking on the track name from > the Assembly browser graphic page view). With this option, you can link in > related tables, customize the format of the output, save results back into > the browser as a custom track, and other functions. Help with examples: > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html > > MySQL: > Instructions -> in the link download29 you had in your original email > (below). Using the table browser to understand the table names, the schema, > what linked tables are also a part of the track, and example data can be > helpful before building a query if it is complex. > > Useful tables to link in alternate/gene names or symbols: kgXref, kgAlias > > To find out more about the output formats, go into the FAQ section and click > into "Data file formats". > > Hopefully this will get you started, > Jennifer > > > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Peng Yu" <[email protected]> wrote: > >> From: "Peng Yu" <[email protected]> >> To: [email protected] >> Sent: Monday, November 30, 2009 9:04:30 AM GMT -08:00 US/Canada Pacific >> Subject: [Genome] How to download the exon regions (start and end positions) >> of all genes? (mouse) >> >> http://genome.ucsc.edu/FAQ/FAQdownloads#download29 >> http://genome.ucsc.edu/cgi-bin/hgTables?org=Mouse >> >> I feel that I might be able to do the query by sql or tab browser to >> find the start and end positions of all the exons (mouse). But I'm >> not >> sure how to do it. Would you please give me some detailed >> instructions >> on this? >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
