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/snp130Exceptions.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
>
> _______________________________________________
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>

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