Hi Joshua, Gene exon information can also be obtained via the Table Browser. In this case, you will need to choose the "Genes and Gene Prediction Tracks" group, and then choose a gene set to use. To get more information about any of the gene tracks, select the track in the Table Browser, and then hit the "describe table schema" button. Once you have selected a gene track, set the output format to "selected fields from primary and related tables". This will allow you to select only the fields you are interested in.
For more general instructions on using the table browser, see: Table Browser User Guide: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Video tutorial: http://www.openhelix.com//cgi/tutorialInfo.cgi?id=28 (click the "Launch" online tutorial button) -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/08/10 13:26, qcshare wrote: >> Hello, >> >> I want to download exons and introns information from the > UCSC, the format like this: > >> Chr Gene name exon start position exon end positon >> chr1 VDR 82938023 829387892 >> chr2 COLIA1 78989087 78989298 >> ..... >> ..... >> >> Could you please tell me how can I download these information. >> Thanks very much. >> >> Joshua. >> >> >> >> On Wed, Sep 29, 2010 at 1:36 AM, Mary Goldman <[email protected]> wrote: >> >>> Hi Joshua, >>> >>> The easiest way to download all the CpG Islands with their coordinates and >>> names is to use the table browser ( >>> http://genome.ucsc.edu/cgi-bin/hgTables). First, select the clade, genome >>> and assembly of interest. Next, select "Regulation" from the group pull-down >>> menu and "CpG Islands" from the track pull-down menu. Select "selected >>> fields from primary and related tables" as the output format, enter a name >>> for the output file if you would like (leave blank to keep output in >>> browser), and click "get output". Select the "chrom", "chromStart", >>> "chromEnd" and "name" check boxes and click "get output". >>> >>> I hope this information is helpful. Please feel free to contact the mail >>> list again if you require further assistance. >>> >>> Best, >>> Mary >>> ------------------ >>> Mary Goldman >>> UCSC Bioinformatics Group >>> >>> >>> On 9/27/10 9:07 PM, qcshare wrote: >>> >>>> Dear Professor, >>>> I want to download the genome CpG islands information, such as the number >>>> of >>>> chromosome, start/end position of the CpG islands and CpG islands ID >>>> numbers, I just found the first three items, but I can not found the >>>> information of CpG islands ID numbers. >>>> Could you please tell me where can I get this information? >>>> >>>> Thank you very much! >>>> >>>> Your Sincerely! >>>> >>>> Joshua. >>>> _______________________________________________ >>>> 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
