Hi, Brooke: I really appreciate your detailed explanation, and it does make a lot of sense.
However, we use the SNP table from UCSC quite heavily in our research and we'd also like to use the latest dbSNP update (version 131). The vast majority of the genome browser's functional tracks that we use, like ENCODE, transcription regulation and expression, to name a few, exist only in hg18. Therefore, we can not switch to hg19 at this time. The data would be much more useful to us and the research community if the latest dbSNP update could also be applied to hg18. I'd really appreciate it if the UCSC team would consider update hg18 with the latest dbSNP release. Xinwei -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Tuesday, July 06, 2010 5:48 PM To: She, Xinwei Cc: Vanessa Kirkup Swing; [email protected] Subject: Re: [Genome] dbSNP 131 for hg18? Hi Xinwei, It is true that UCSC realigns the flanking sequences from dbSNP, but these realignments are not used to determine genomic location. In fact, for each SNP, the realignment is only done between the flanking sequence from dbSNP and the genomic region immediately surrounding the location determined by dbSNP. We do this to try to provide useful information in the case where there is conflicting information about a SNP (for instance, when class is listed as "single", but the position spans more than one base). The genomic coordinates of the SNPs displayed in the Genome Browser come directly from dbSNP. I hope this is helpful. Please let us know if we can clarify further. -- Brooke Rhead UCSC Genome Bioinformatics Group She, Xinwei wrote on 7/6/10 1:29 PM: > Hi, Vanessa: > > Thanks for your answer. However, as far as I know, UCSC realigned the > flanking sequences of SNPs to determine their genomic locations: > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=164326263&o=33034697&t=33034698 > &g=snp131&i=rs7510525 > > And that's why I was asking about SNP 131 on hg18, because I'd prefer > using UCSC's SNP coordinates. > > > Xinwei > > -----Original Message----- > From: Vanessa Kirkup Swing [mailto:[email protected]] > Sent: Friday, July 02, 2010 6:39 PM > To: She, Xinwei > Cc: [email protected] > Subject: Re: [Genome] dbSNP 131 for hg18? > > Dear Xinwei, > > We obtain all of our SNP mappings directly from dbSNP, and thus will > only provide a SNP131 track on hg18 if dbSNP provides the mappings. The > other option is to do a lift down using our liftover tool: > http://genome.ucsc.edu/cgi-bin/hgLiftOver > > If you have further questions, please don't hesitate to contact the > mailing list again. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > ----- Original Message ----- > From: "Xinwei She" <[email protected]> > To: [email protected] > Sent: Friday, July 2, 2010 10:39:21 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] dbSNP 131 for hg18? > > Hi, there: > > It great to see UCSC genome browser has released dbSNP 131 for hg19. > However, right now vast majority of the functional genomic tracks are > still in hg18, e.g.. the ENCODE tracks. The genomics community are still > mainly working on hg18. I'm just wondering if UCSC has a plan to release > dbSNP 131 for hg18, as well? > > Xinwei > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you > are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. 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