Hi Pravin, The snp130 table only contains information from dbSNP. That said, there is a lot more information in the dbSNP records than is included in the table -- we have selected only a subset of information to include. You can see the files at dbSNP that we used as sources under "Data Sources" header on the track description page.
Another way to download the complete table is from our downloads page. From the homepage, click on Downloads -> Human -> (scroll to hg18) -> Annotation Database -> snp130.txt.gz This will take you to the following location: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz I hope this is helpful. Please feel free to send any further questions to [email protected] -- Brooke Rhead UCSC Genome Bioinformatics Group PRAVIN wrote on 10/2/10 11:08 PM: > 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 >> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
