Thanks, very helpful! Paul
On Mar 23, 2009, at 6:25 PM, Jennifer Jackson wrote: > Hello Paul, > Yes, there is a sanity check as part of the process. Please examine > a SNP's details page for information about surrounding sequence, SNP > type, multiple hit locations, or other quality metrics. For the SNPs > that are absent, from examination, it appears that many map to > alternate versions of genomic (Celera, HuRef) or are noted as "no > link established by analysis of contig annotation". One of our > developer's suggests reviewing the dbSNP report as it has > interesting information/statistics down in the GeneView section. > Thank you for following up and getting the full answer. This > information will also help many other data users. > Jennifer Jackson > UCSC Genome Bioinformatics Group > > > > Paul de Bakker wrote: >> 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
