[BioC] where to get chr_rpts file for dbSNP human 36.3 assembly

[shirley zhang]

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?

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
>>
>> _______________________________________________
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>>
>



-- 
Xiaoling (Shirley) Zhang

M.D., Ph.D. (Bioinformatics)
Boston University, Boston, MA
Tel: (857) 233-9862
Email: zhangxl at bu.edu