Hi Gung-wei, You can find 'cdsStart' and 'cdsEnd' in the 'xenoRefGene' table.
Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 8/30/2011 7:24 AM, Gung-wei Chirn wrote: > Hi Greg, > > A quick question. > When I select xenoRefSeqAli from Rat genome under "Other Refseq", I couldn't > select cds information. > > Is there a way to get cds? or I need to select other tables? > > Thanks, > > Gung-wei > > On Wed, Aug 24, 2011 at 9:47 PM, Gung-wei Chirn<[email protected]> wrote: > >> Hi Greg, >> >> Thank you so much. I am able to obtain the information i need. >> really helpful. >> >> Best, >> >> Gung-wei >> >> >> On Mon, Aug 22, 2011 at 7:03 PM, Greg Roe<[email protected]> wrote: >> >>> Hi Gung-wei, >>> >>> I did indeed misread your question. Since you're referring to the OTHER - >>> RefSeq table, yes, let me explain how to get that information from the table >>> browser. >>> >>> - For output format, select: selected fields from primary and related >>> tables. Then, get output. >>> - On the next page under the Linked tables, select "gbCdnaInfo" and click >>> "Allow Selection From Checked Tables". >>> - Now that that table's checked, again under Linked tables, select the >>> table "organism" and click "Allow Selection From Checked Tables". >>> >>> Finally, you can now select the fields you need from the main table >>> "oryCun2.refGene" that you want, plus select the "name/Associated text" >>> frield from the "oryCun2.organism fields" table. "Get output" will now >>> display the data with the organism field. >>> >>> - Greg >>> >>> >>> >>> On 8/22/11 3:35 PM, Greg Roe wrote: >>> >>>> Hi Gung-wei >>>> >>>> Maybe I'm misunderstanding your question, but if you're downloading the >>>> table into bed format using the table browser, the first thing you must >>>> select at the top is what species/assembly your wanting to view/download >>>> data from. So once you click "get output" you are downloading only >>>> tables/data for that selected assembly. >>>> >>>> You are correct that there is no species information in the data itself. >>>> However, knowing that you downloaded it from, for example, the oryCun2 >>>> (rabbit) database, you know that you have rabbit data. If you've >>>> download a bed file, you may want to name the file something descriptive >>>> like, "oryCun2_refGene.bed", for example. >>>> >>>> Please let us know if you have any additional questions: >>>> [email protected] >>>> >>>> - >>>> Greg Roe >>>> UCSC Genome Bioinformatics Group >>>> >>>> >>>> >>>> On 8/22/11 11:38 AM, Gung-wei Chirn wrote: >>>> >>>>> Dear UCSC Genome Browser team, >>>>> >>>>> I am a bioinformatician at Brandeis Unoversity, Waltham MA USA. >>>>> >>>>> We are trying to down load the table of<<Rabbit - Other RefSeq tables>> >>>>> in >>>>> bed format. >>>>> However, the species information is not included in the table. (see >>>>> below) >>>>> >>>>> chr1 51507 53374 RNF183 0 + 52452 53037 0 >>>>> 5 18,99,397,155,94, 0,28,933,1378,1773, >>>>> chr1 51744 53331 RNF183 0 + 52452 53037 0 >>>>> 4 21,391,189,88, 0,702,1110,1499, >>>>> chr1 52452 53296 RNF183 0 + 52452 53037 0 >>>>> 6 385,165,11,18,23,24, 0,429,623,664,783,820, >>>>> >>>>> We are able to see Homo/Bos/Mus indicated on the genome browser, but not >>>>> in >>>>> the download table. >>>>> We also tried different tables, but still can not find the species >>>>> information. >>>>> >>>>> Could you please help us to obtain such information? >>>>> >>>>> Thanks, >>>>> >>>>> Gung-wei Chirn >>>>> 781-325-8088 >>>>> Bioinformatician at Biology Department >>>>> Brandeis University >>>>> Waltham, MA USA >>>>> ______________________________**_________________ >>>>> Genome maillist - [email protected] >>>>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>>>> >>>> ______________________________**_________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<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
