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

[shirley zhang]

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
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> 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