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
