Hello Paul, We get everything in the snp129 table directly from dbSNP. (Look in the "Data Sources" section for details.)
However when you click through to the details page, we do re-align the flanking sequences to the genomic (see "UCSC Re-alignment of flanking sequences"). And you are correct, the strand field means genomic strand. We save most of our coordinates (including these) with respect to the (+) strand, so you don't need to do anything if that is what you want. Coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Paul de Bakker wrote: > What I really want to know what I need to do to get the listed alleles > to be oriented on the fwd/+ strand? > > Do you internally align the dbSNP fasta sequences to the hg18 to > ascertain the "strand" or are these records straight copies from dbSNP? > > Thanks! > Paul > > > On Mar 22, 2009, at 11:51 AM, Paul de Bakker wrote: > > >> Hi [email protected] >> >> I have downloaded the dbSNP129 data from the Table browser >> (database: hg18) and I wanted to check with you that the listed >> "strand" field refers to the + or - strand of the genome assembly >> (i.e. hg18)? That is, if I make everything on the + strand I >> only need to flip the Watson-Crick bases for the SNPs where strand = >> "-"? >> >> Thanks >> Paul >> >> > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
