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
