Hi Kyle, I have an important correction to communicate. UCSC does place SNPs on the genomic reference sequence. Instead, our alignments are generated as part of the Browser display only. All placements are derived from dbSNP.
This is from the track description page: UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. dbSNP's flanking sequences are in ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/rs_fasta/ You may still find it useful to use BLAT as a back-up check or to gather the types of statistics/alignments available in the Browser, but we wanted to make the distinction very clear between what processing is done by UCSC and what is published as released from dbSNP. Very sorry for any confusion, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Kyle Tretina" <[email protected]> > Cc: "UCSC" <[email protected]> > Sent: Tuesday, January 5, 2010 12:41:20 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Automation Question > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
