Hi Jennifer: So based on your re-alignments, do you correct the strand field if the strand reported by dbSNP was wrong?
I have 282 SNPs that have a valid entry in dbSNP (by using their browser) but do not appear in the dbSNP129 table in UCSC. http://www.broad.mit.edu/~debakker/282_not_annotated_snps.txt Any chance you could help me figure out why these do not appear? Best wishes, Paul On Mar 23, 2009, at 2:59 PM, 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
