Hello again, I imagine that this is becoming frustrating to you, but I need to state again that data available from other public projects is not always included in entirety in the UCSC browser.
For your question, this means that if the data related to a particular GeneID is not in the tables, then the data is not in the UCSC browser. You can read the UCSC Gene's and RefSeq Gene's track descriptions for a general overview of our processing, but you will not find the exact reason for specfic examples being present/not present. A reasonable alternative is to use the UCSC Genes track directly. It is a comprehensive, non-redundant representation of all known genes from multiple input sources. RefSeq is one of the inputs, so you do not need to do both. Or, if you really want the data as organized by the external project in entirety, perhaps try the original source of the data? If all they have is mRna or protein sequence, you can always run your own BLAT and create a custom track. Or maybe they have alignment data available that you could use to extract the exon information or you could convert to one of the custom track formats and upload to use our other tools. Check the FAQ section for help with BLAT and Custom tracks. I hope this gives you a better understanding of how the data is organized and some options for a solution that meets your research goals, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Peng Yu" <[email protected]> wrote: > From: "Peng Yu" <[email protected]> > To: [email protected] > Sent: Wednesday, December 2, 2009 3:41:43 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] How to download the exon regions (start and end > positions) of all genes? (mouse) > > 'select locusLinkId as geneId, refFlat.* > from refFlat inner join refLink > on refFlat.name = refLink.mrnaAcc > ;' > > I use the above command to get the exon information for a give Gene > ID. But since some Gene IDs are missing as shown in the following > message, I'm wondering how to get the exon information for all the > known Gene IDs. > > https://lists.soe.ucsc.edu/pipermail/genome/2009-December/020652.html > > 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 > > > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
