Hello Kyle, The best place to start is by reading the methods used for the SNP track. These are contained in the track description page (click through the dbSNP track label in the Assembly browser).
The SNP data from UCSC will be the filtered set (only those that passed our criteria, as defined in the methods). The best place to get the complete SNP release data is directly from dbSNP. http://www.ncbi.nlm.nih.gov/projects/SNP/ Genomic can also be retrieved from NCBI or from our downloads server (we offer a few alternate format choices). As described in the methods, we use BLAT to do the alignment and it works very well, so using BLAT is the recommendation. The results can be filtered to eliminate those that include mismatches using your own tools (the number of mismatches is one of the fields you can include in the output). Genomic download at UCSC: http://hgdownload.cse.ucsc.edu/downloads.html -> organism common name -> assembly release -> Full data set http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download Instructions for obtaining BLAT and links to associated documentation: http://genome.ucsc.edu/FAQ/FAQblat Good luck, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Kyle Tretina" <[email protected]> wrote: > From: "Kyle Tretina" <[email protected]> > To: "UCSC" <[email protected]> > Sent: Tuesday, January 5, 2010 12:00:52 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Automation Question > > UCSC, > > I wish to attempt to batch automate the re-alignment of SNP > flanking > sequences to the genomic sequence similar to the way that you do on > your > website and I have two questions. I already have the list of rs > numbers that > correspond to all of the SNP's that I wish to use, but in the > alignment I > only want the sequence around the SNP that has no mismatches with the > genomic sequence. > > 1) Where can I batch download the dbSNP flanking sequences? > 2) Where can I download the corresponding genomic sequence? > 3) How would you recommend I go about this re-alignment (i.e. what > program/general procedure) > > > Thank you for your assistance. > > Kyle Tretina > Wheaton College > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
