Hello, Sir, I need your help. Now, I want to get the intron genome information, the formate like this.
Chr number Gene name TSS TTS start position end position Thanks very much for your kind help. Joshua. On Thu, Nov 11, 2010 at 5:58 AM, Brooke Rhead <[email protected]> wrote: > Hi Joshua, > > Thank you for your question. In order to receive an answer in the timeliest > manner and for the benefit of all of our users, for whom we try to have the > most comprehensive archives, I would appreciate it if you resent your email > to [email protected]. In this way, users with similar problems will be > able to benefit from your question and our answers. Thank you for your > understanding in this matter. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 11/10/10 13:30, qcshare wrote: > >> Hello Brooke, >> but I did not find the introns data. >> Could you please point it out for me? >> Thanks. >> >> On Tue, Nov 9, 2010 at 7:08 AM, Brooke Rhead <[email protected]> wrote: >> >> Hi Joshua, >>> >>> Gene e >>> >> >> >> >> xon 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
