Great. Got it! Thanks. Gung-wei
On Tue, Aug 30, 2011 at 5:53 PM, Luvina Guruvadoo <[email protected]>wrote: > 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> >>>>>> <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> >>>>> <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
