Hi Kyle, I assume you're referring to the "Re-alignment of the SNP's flanking sequences to the genomic sequence" section of the details page that appears when you click on a SNP, correct me if I'm wrong.
Yes, the masking information should be the same -- it is taken directly from the reference assembly sequence file named in the chromInfo table. For example, if your mirror has the hg19 database, and you execute "select fileName from hg19.chromInfo limit 1;" in mysql, the result is "/gbdb/hg19/hg19.2bit" (unless you use a different path locally). If that file is up-to-date with our download site (which it should be; I'm not aware of any instance of our changing the masking of the assembly sequence file(s) after initial release), it contains the same masking information. If you find a counterexample, or if that's not the alignment you're referring to, please let us know! Angie ----- "Kyle Tretina" <[email protected]> wrote: > From: "Kyle Tretina" <[email protected]> > To: [email protected], "Pattle Pun" <[email protected]> > Sent: Thursday, February 4, 2010 6:59:33 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Automation Question > > To whom it may concern, > > The principle investigator of my research team wonders if, by using the data > from the dbSNP130 track, all of the masking information will be included > just like when an SNP is manually entered into the website. Primarily, I > believe his concern is whether a mirror using that track will yield the same > alignment results as when an rs number is entered manually into the database > in general. Could you please clear this up for us? > > > Kyle Tretina > Wheaton College > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
