Dear Herve, Sean, and All After updating my R, now I can use the liftOver() in rtracklayer package. However I met a problem for SNP rs171. It is on chr 1 in build37.3, but on chr7 in build 36.3. Please check the following link: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=171 In this case, does liftOver work? How many SNPs in NCBI dbSNP like this, map to different chr between different builds. Thanks, Shirley On Thu, Nov 3, 2011 at 2:16 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, Nov 3, 2011 at 2:05 PM, shirley zhang <shirley0818 at="" gmail.com=""> wrote: >> Dear Herve and Sean, >> >> Thanks for your reply. ?May I ask one more help from you? >> >> Do you know where I can get the list of SNPs (rs# ) mapped to more >> than 1 location on the reference genome NCBI Build 36.3? > > Hi, Shirley. ?This level of detail might need to go to NCBI for an > answer if you REALLY need to use NCBI annotations directly. ?That > said, UCSC does some reannotation before releasing dbSNP on their > site. ?There is a table that described dbSNP exceptions including > Multiple Locations. ?You can download that file here: > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Except ions.txt.gz > > The table format is described here: > > http://genome.ucsc.edu/cgi- bin/hgTables?hgta_doSchemaDb=hg18&hgta_doSchemaTable=snp130Exceptions > > Sean > > >> Thanks, >> Shirley >> >> On Tue, Nov 1, 2011 at 9:20 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>> 2011/11/1 shirley zhang <shirley0818 at="" gmail.com="">: >>>> Dear Hever, >>>> >>>> Also, I just checked that there is no liftOver function in the >>>> rtracklayer package. Is it a different function name? ?Thanks, Shirley >>>> >>>>> sessionInfo() >>>> R version 2.11.1 (2010-05-31) >>> >>> Hi, Shirley. >>> >>> You'll definitely need to update your R. ?R was just released and is >>> now at version 2.14.0. ?With the new version of R, you'll get new >>> versions of packages. ?The most recent couple of versions of >>> rtracklayer include liftover() >>> >>> Sean >>> >>> >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C >>>> ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 >>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 >>>> ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C >>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] rtracklayer_1.8.1 RCurl_1.4-3 ? ? ? bitops_1.0-4.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.8.0 ? ? ? Biostrings_2.16.9 ? BSgenome_1.16.5 >>>> [4] GenomicRanges_1.0.9 IRanges_1.6.15 ? ? ?XML_3.1-1 >>>> >>>> >>>> 2011/11/1 shirley zhang <shirley0818 at="" gmail.com="">: >>>>> Dear Herve, >>>>> >>>>> Thanks for your quick response. >>>>> >>>>> I need to get the chr position (hg18, build36.3) ?for a huge list of >>>>> SNPs with rs#. As you suggested before, I first tried the library >>>>> "SNPlocs.Hsapiens.dbSNP.20090506", and got the chr position for 90% of >>>>> my SNPs. For the remaining 10% of SNPs, I would like to get the chr >>>>> position from the NCBI dbSNP website ( build 130, reference 36.3). I >>>>> understand that I could use the batch query. However, I have to do >>>>> this kind of mapping routinely for different sets of SNPs. So I am >>>>> thinking to download those chr_rpts files for dbSNP human 36.3 >>>>> assembly to our server, then use them to do the mapping. >>>>> >>>>> I don't know what I've tried or will going to do is the right way to >>>>> do. Could you give me any comments or suggestions? >>>>> >>>>> Thanks a lot! >>>>> Shirley >>>>> >>>>> 2011/11/1 Hervé Pagès <hpages at="" fhcrc.org="">: >>>>>> Hi Shirley, >>>>>> >>>>>> On 11-11-01 01:51 PM, shirley zhang wrote: >>>>>>> >>>>>>> Dear list, >>>>>>> >>>>>>> In terms of dbSNP database in NCBI, I can get the chr_rpts files for >>>>>>> the most recent 37.3 assembly from the following FTP site, >>>>>>> >>>>>>> ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/ >>>>>>> >>>>>>> My question is how/where I can get these chr_rpts files based on the >>>>>>> 36.3 assembly >>>>>> >>>>>> Please don't cross post. This sounds like a question for the dbSNP >>>>>> folks. >>>>>> >>>>>> FWIW, right now it doesn't seem like those files have been updated yet: >>>>>> they are still from August 15 (i.e. dbSNP build 134, based on reference >>>>>> genome GRCh37.p2). AFAIK the last build based of the 36.3 assembly was >>>>>> dbSNP build 130. >>>>>> >>>>>> Not sure what you want to do with those files, but if you only need >>>>>> to access the genome coordinates and alleles of your SNPs, you might >>>>>> want to have a look at the SNPlocs.* packages. >>>>>> >>>>>> Alternatively, you could always use a tool like UCSC liftOver (also >>>>>> available in Bioconductor, in the rtracklayer package) to remap things >>>>>> between different genome assemblies. >>>>>> >>>>>> Cheers, >>>>>> H. >>>>>> >>>>>>> >>>>>>> Thanks, >>>>>>> Shirley >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>>> -- >>>>>> Hervé Pagès >>>>>> >>>>>> Program in Computational Biology >>>>>> Division of Public Health Sciences >>>>>> Fred Hutchinson Cancer Research Center >>>>>> 1100 Fairview Ave. N, M1-B514 >>>>>> P.O. Box 19024 >>>>>> Seattle, WA 98109-1024 >>>>>> >>>>>> E-mail: hpages at fhcrc.org >>>>>> Phone: ?(206) 667-5791 >>>>>> Fax: ? ?(206) 667-1319 >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Xiaoling (Shirley) Zhang >>>>> >>>>> M.D., Ph.D. (Bioinformatics) >>>>> Boston University, Boston, MA >>>>> Tel: (857) 233-9862 >>>>> Email: zhangxl at bu.edu >>>>> >>>> >>>> >>>> >>>> -- >>>> Xiaoling (Shirley) Zhang >>>> >>>> M.D., Ph.D. (Bioinformatics) >>>> Boston University, Boston, MA >>>> Tel: (857) 233-9862 >>>> Email: zhangxl at bu.edu >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >> >> >> >> -- >> Xiaoling (Shirley) Zhang >> >> M.D., Ph.D. (Bioinformatics) >> Boston University, Boston, MA >> Tel: (857) 233-9862 >> Email: zhangxl at bu.edu >> > -- Xiaoling (Shirley) Zhang M.D., Ph.D. (Bioinformatics) Boston University, Boston, MA Tel: (857) 233-9862 Email: zhangxl at bu.edu

The liftOver function can indeed map between chromosomes. On Fri, Nov 4, 2011 at 8:27 AM, shirley zhang <shirley0818@gmail.com> wrote: > Dear Herve, Sean, and All > > After updating my R, now I can use the liftOver() in rtracklayer > package. However I met a problem for SNP rs171. It is on chr 1 in > build37.3, but on chr7 in build 36.3. Please check the following link: > > http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=171 > > In this case, does liftOver work? How many SNPs in NCBI dbSNP like > this, map to different chr between different builds. > > Thanks, > Shirley > > > On Thu, Nov 3, 2011 at 2:16 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > On Thu, Nov 3, 2011 at 2:05 PM, shirley zhang <shirley0818@gmail.com> > wrote: > >> Dear Herve and Sean, > >> > >> Thanks for your reply. May I ask one more help from you? > >> > >> Do you know where I can get the list of SNPs (rs# ) mapped to more > >> than 1 location on the reference genome NCBI Build 36.3? > > > > Hi, Shirley. This level of detail might need to go to NCBI for an > > answer if you REALLY need to use NCBI annotations directly. That > > said, UCSC does some reannotation before releasing dbSNP on their > > site. There is a table that described dbSNP exceptions including > > Multiple Locations. You can download that file here: > > > > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Except ions.txt.gz > > > > The table format is described here: > > > > > http://genome.ucsc.edu/cgi- bin/hgTables?hgta_doSchemaDb=hg18&hgta_doSchemaTable=snp130Exceptions > > > > Sean > > > > > >> Thanks, > >> Shirley > >> > >> On Tue, Nov 1, 2011 at 9:20 PM, Sean Davis <sdavis2@mail.nih.gov> > wrote: > >>> 2011/11/1 shirley zhang <shirley0818@gmail.com>: > >>>> Dear Hever, > >>>> > >>>> Also, I just checked that there is no liftOver function in the > >>>> rtracklayer package. Is it a different function name? Thanks, Shirley > >>>> > >>>>> sessionInfo() > >>>> R version 2.11.1 (2010-05-31) > >>> > >>> Hi, Shirley. > >>> > >>> You'll definitely need to update your R. R was just released and is > >>> now at version 2.14.0. With the new version of R, you'll get new > >>> versions of packages. The most recent couple of versions of > >>> rtracklayer include liftover() > >>> > >>> Sean > >>> > >>> > >>>> x86_64-unknown-linux-gnu > >>>> > >>>> locale: > >>>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > >>>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 > >>>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C > >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C > >>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > >>>> > >>>> attached base packages: > >>>> [1] stats graphics grDevices utils datasets methods base > >>>> > >>>> other attached packages: > >>>> [1] rtracklayer_1.8.1 RCurl_1.4-3 bitops_1.0-4.1 > >>>> > >>>> loaded via a namespace (and not attached): > >>>> [1] Biobase_2.8.0 Biostrings_2.16.9 BSgenome_1.16.5 > >>>> [4] GenomicRanges_1.0.9 IRanges_1.6.15 XML_3.1-1 > >>>> > >>>> > >>>> 2011/11/1 shirley zhang <shirley0818@gmail.com>: > >>>>> Dear Herve, > >>>>> > >>>>> Thanks for your quick response. > >>>>> > >>>>> I need to get the chr position (hg18, build36.3) for a huge list of > >>>>> SNPs with rs#. As you suggested before, I first tried the library > >>>>> "SNPlocs.Hsapiens.dbSNP.20090506", and got the chr position for 90% > of > >>>>> my SNPs. For the remaining 10% of SNPs, I would like to get the chr > >>>>> position from the NCBI dbSNP website ( build 130, reference 36.3). I > >>>>> understand that I could use the batch query. However, I have to do > >>>>> this kind of mapping routinely for different sets of SNPs. So I am > >>>>> thinking to download those chr_rpts files for dbSNP human 36.3 > >>>>> assembly to our server, then use them to do the mapping. > >>>>> > >>>>> I don't know what I've tried or will going to do is the right way to > >>>>> do. Could you give me any comments or suggestions? > >>>>> > >>>>> Thanks a lot! > >>>>> Shirley > >>>>> > >>>>> 2011/11/1 Hervé Pagčs <hpages@fhcrc.org>: > >>>>>> Hi Shirley, > >>>>>> > >>>>>> On 11-11-01 01:51 PM, shirley zhang wrote: > >>>>>>> > >>>>>>> Dear list, > >>>>>>> > >>>>>>> In terms of dbSNP database in NCBI, I can get the chr_rpts files > for > >>>>>>> the most recent 37.3 assembly from the following FTP site, > >>>>>>> > >>>>>>> ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/ > >>>>>>> > >>>>>>> My question is how/where I can get these chr_rpts files based on > the > >>>>>>> 36.3 assembly > >>>>>> > >>>>>> Please don't cross post. This sounds like a question for the dbSNP > >>>>>> folks. > >>>>>> > >>>>>> FWIW, right now it doesn't seem like those files have been updated > yet: > >>>>>> they are still from August 15 (i.e. dbSNP build 134, based on > reference > >>>>>> genome GRCh37.p2). AFAIK the last build based of the 36.3 assembly > was > >>>>>> dbSNP build 130. > >>>>>> > >>>>>> Not sure what you want to do with those files, but if you only need > >>>>>> to access the genome coordinates and alleles of your SNPs, you might > >>>>>> want to have a look at the SNPlocs.* packages. > >>>>>> > >>>>>> Alternatively, you could always use a tool like UCSC liftOver (also > >>>>>> available in Bioconductor, in the rtracklayer package) to remap > things > >>>>>> between different genome assemblies. > >>>>>> > >>>>>> Cheers, > >>>>>> H. > >>>>>> > >>>>>>> > >>>>>>> Thanks, > >>>>>>> Shirley > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Bioconductor mailing list > >>>>>>> Bioconductor@r-project.org > >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>>>> Search the archives: > >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>>>> > >>>>>> > >>>>>> -- > >>>>>> Hervé Pagčs > >>>>>> > >>>>>> Program in Computational Biology > >>>>>> Division of Public Health Sciences > >>>>>> Fred Hutchinson Cancer Research Center > >>>>>> 1100 Fairview Ave. N, M1-B514 > >>>>>> P.O. Box 19024 > >>>>>> Seattle, WA 98109-1024 > >>>>>> > >>>>>> E-mail: hpages@fhcrc.org > >>>>>> Phone: (206) 667-5791 > >>>>>> Fax: (206) 667-1319 > >>>>>> > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Xiaoling (Shirley) Zhang > >>>>> > >>>>> M.D., Ph.D. (Bioinformatics) > >>>>> Boston University, Boston, MA > >>>>> Tel: (857) 233-9862 > >>>>> Email: zhangxl@bu.edu > >>>>> > >>>> > >>>> > >>>> > >>>> -- > >>>> Xiaoling (Shirley) Zhang > >>>> > >>>> M.D., Ph.D. (Bioinformatics) > >>>> Boston University, Boston, MA > >>>> Tel: (857) 233-9862 > >>>> Email: zhangxl@bu.edu > >>>> > >>>> _______________________________________________ > >>>> Bioconductor mailing list > >>>> Bioconductor@r-project.org > >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>> > >>> > >> > >> > >> > >> -- > >> Xiaoling (Shirley) Zhang > >> > >> M.D., Ph.D. (Bioinformatics) > >> Boston University, Boston, MA > >> Tel: (857) 233-9862 > >> Email: zhangxl@bu.edu > >> > > > > > > -- > Xiaoling (Shirley) Zhang > > M.D., Ph.D. (Bioinformatics) > Boston University, Boston, MA > Tel: (857) 233-9862 > Email: zhangxl@bu.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]