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 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
