Hello again Meharji, It sounds like you might have been retrieving BED output. In the Table Browser try selecting:
output format: "all fields from selected table" to get all the columns of this table. or output format: "selected fields from primary and related tables" if you want a subset of the data. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 08/03/11 09:35, Meharji Arumilli wrote: > On 7/15/11 2:27 AM, Vanessa Kirkup Swing wrote: >> Hi Meharji, >> >> We have a track for snp131 on the genome preview browser. Just keep in >> mind that tracks on the preview browser have not undergone thorough >> testing and may change: >> >> http://genome-preview.ucsc.edu/cgi-bin/hgGateway?org=Dog&db=canFam2&hgsid=2566535 >> >> You may also download the data by using the Table Browser on genome-preview: >> >> http://genome-preview.ucsc.edu/cgi-bin/hgTables >> >> Select canFam2, group: Variation and repeats, track: snp131, table: >> snp131. You can select various output formats. Downloading the whole >> db131 table in BED format is about 28.3 MB in size. >> >> If you have additional questions, please contact the mailing list: >> [email protected]. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ---------- Forwarded message ---------- >> From: Meharji Arumilli<[email protected]> >> Date: Thu, Jul 14, 2011 at 4:16 AM >> Subject: [Genome] dbSNP for canFam2 >> To: [email protected] >> >> >> Hi, >> >> I working with dog sequencing data and using canFam2 build for my work. >> I am in need of dbSNP database for canFam2 build which i cannot find in >> the databases present in canFam2. I could find it in canFam1 but not in >> canFam2. Could you please recommend anything regarding this or is there >> any option available to convert dbSNP from canFam1 to canFam2 ? Looking >> forward to hearing from you at the latest. >> >> Thank you >> >> >> Best regards >> mehar >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > Thanks for your reply. I have downloaded the data from the link, > > http://genome-preview.ucsc.edu/cgi-bin/hgTables > > But the data in canFam2 snp 131 contains only six columns(does not have > reference allele, observed allele....) whereas the data in canFam1 > snp125 contains 16 columns. For my work i need the data in the format > which is exactly present in snp125, any help regarding this would be > appreciated. > > Looking forward to hearing from you. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
