Dear Vanessa, I only want complete dbSNP records from build 130 of assembly HG18 (human). When we use tables, are we getting data completely from dbSNP or is it a mixture of other database also. I want dbSNP records only. So how could i go forward with this.
Regards, Pravin Nilawe On Sat, Oct 2, 2010 at 2:08 AM, Vanessa Kirkup Swing <[email protected]>wrote: > Dear Pravin, > > A good way to find out information about a table is to look at the table > schema for that track. To do this you can either use the table browser ( > http://genome.ucsc.edu/cgi-bin/hgTables) or by going to the track > description page ( > http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr21&g=snp130). > > > If you decide to use the table browser: > > 1) Select the appropriate clade, genome, assembly, group, track, and table. > > 2) Click on "describe table schema" > > This will give you the fields for the primary table and also will give you > the the connected tables and joining fields. > > > If you decide to use the description page, scroll down the page and click > on "View table schema". Also, the description page also is a very good > resource for explaining the data that is in the table that you are > interested in. > > > To get only the dbSNP ids for build 130 you will need to use the table > browser to download the information. > > Set the following fields: > > clade: Mammal > genome: Human > assembly: hg19 > group: Variations and Repeats > track: SNPs 130 > table: snp130 > region: genome > output format: selected fields from primary and related tables > output file: fileName if you would like to save it to your computer. > > Click on "get output" > > Check "name" and any other fields that you are interested in. > > Click on "get output" > > I hope that this helps! Feel free to contact the mailing list if you have > further questions. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "PRAVIN" <[email protected]> > To: [email protected] > Sent: Thursday, September 30, 2010 1:38:48 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] SNP track & link between builds. > > Hello, > > I going through Tables available at the website and had few questions for > SNP download. > > If I want to download snp130 table from the web, will i get records from > dbSNPs. If no then which is the other data involved along with this build. > > how could i get only dbsnp ids of build 130? > > can i download it through tables. > -- > Pravin Nilawe > Bioinformatics, > +91 9869739671 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- Pravin Nilawe Bioinformatics, +91 9869739671 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
