Hi Paul, A couple additional comments:
The re-alignment of flanking sequences is not stored in our database -- it is computed dynamically when you view a SNP's details page. It may sometimes look a little inconsistent with dbSNP's mapping, which we think is of interest to users. But again, everything in the snp129 database table is from dbSNP. In the snp129 table, a '-' strand does mean that you should reverse-complement snp129.observed in order to see the bases as they would appear on the + strand. However, the bases in refNCBI and refUCSC are always relative to the + strand, so they should not be rev-comp'd. [snp129.observed sometimes has multi-base variants like -/AAAG/CAA, so if you're not excluding those, flipping each W-C base is not enough -- the order of the bases should be reversed too.] Hope that helps, Angie On Mon, 23 Mar 2009, Jennifer Jackson wrote: > 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 > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
