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

[shirley zhang]

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)
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
>>>
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>>
>>
>> --
>> 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