Hi Ross, There are a few prior mailing list answers that can provide help. For each, substitute the dbSNP build to be "129" and the genome to be March 2006 (hg18).
http://www.soe.ucsc.edu/pipermail/genome/2007-January/012650.html General instructions for obtaining the SNP flanking sequence from the genomic. For you query, paste in the rs numbers into the identifiers filter and set region = genome, name file, and download locally. Click on "describe table schema" to understand formatting and other information linked to this data. Also extract the table to obtain variation(s). Note that the sequence output has the reference genome's sequence. You will need to swap in the SNP variation data for the SNP base position (sometimes this is a deletion) to create the variant fasta sequences using your own tools. Other SNP tracks will also contain data in this format and can be handled the same way. This is probably the best method to get all of the variation data. http://www.soe.ucsc.edu/pipermail/genome/2008-June/016559.html Genomic files in Downloads area with IUPAC substitutions for single-base SNPs only. To extract specific regions from these genomic fasta files once you have them locally: 1) obtain coordinates of SNP(s) from Table browser and expand to be 200 upstream and 200 downstream 2) use the utility faFrag to extract sequence (wrap in a shell/perl/etc. script). This utility is in kent source tree. http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities Help/FAQ links: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/FAQ/FAQdownloads#download27 http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Jennifer Jackson UCSC Genome Bioinformatics Group Ross KK Leung wrote: > Dear all, > > We would like to retrieve flanking sequences at UCSC site, e.g. for > rs17019583: 200 bases upstream, and 200 downstream for a total of 401 bases. > And then save as txt files. > > How can we do that in batch if we have dozens of rs numbers in hand? Thanks > a lot for your advice. > > Best regards, Ross > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
