Thanks, Angie. Paul
On Mar 23, 2009, at 3:42 PM, Angie Hinrichs wrote: > 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
