Hello, To find the data, first go into the Assembly browser and identify the tracks (below) - they will be in the Variation track group. To determine which you want to use, click on the track names to go to a description page that provides the source, methods, and at the top of the page - a link to the primary table (view schema). Click this - it will take you into the Table browser. The page has the primary table, related tables, and the track description again. Click on Tables in the top link to go to the main Table browser form. From here, you can output the data or simply learn what the relevant table(s) are named and how they are related.
If you just want flat files, use the table names from above, and go to the Downloads server. Navigate by common name -> assembly -> annotation database -> <files> The file names are the same as the table names, with a .txt.gz added for the data and .sql added for the schema. Ftp the data to your side. Instructions for Table browser: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser Instructions for Downloading data (ftp or Table browser): http://genome.ucsc.edu/FAQ/FAQdownloads#download1 Table/file format explanations: http://genome.ucsc.edu/FAQ/FAQformat Technical coordinate info: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Gundala Viswanath" <[email protected]> wrote: > From: "Gundala Viswanath" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Thursday, December 3, 2009 12:36:20 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Rare SNPs Annotation in UCSC? > > Dear Ms Jackson, > > > We do have some tracks for datasets with sufficient sample sizes to > estimate frequency within some populations: HGDP Alleles contains > frequencies in 53 > > populations worldwide, and HapMap SNPs includes allele counts (even > better -- you know the sample size in addition to freq) for 11 > populations. > > I think this the one I am looking for. Is there a way I can download > the flat file for it? > Please advice. > > Regards, > G.V. > > > > > > ------------------------------------------------ > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > ----- "Gundala Viswanath" <[email protected]> wrote: > > > >> From: "Gundala Viswanath" <[email protected]> > >> To: [email protected] > >> Sent: Wednesday, December 2, 2009 6:42:46 AM GMT -08:00 US/Canada > Pacific > >> Subject: [Genome] Rare SNPs Annotation in UCSC? > >> > >> Hi, > >> > >> I have no problem downloading human (hg19) snp annotation here: > >> > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp130.txt.gz > >> > >> Currently I am looking for the same annotation file for Rare SNPs. > >> Is there a way to download them that in UCSC? > >> > >> > >> - G.V. > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
