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Question: Accessing SNP datasets from NCBIM37 on biomaRt
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gravatar for Rob
8 weeks ago by
Rob0
Rob0 wrote:

Hi,

I am trying to search for SNPs within a region of the NCBIM37 mouse build using biomaRt. I have been able to access the build for the purposes of locating genes with this region using the answer from a previous question on this forum, but can't seem to find the dataset containing SNP information. Is this available? Thank you very much!

Rob

 

The code I have used to access the build so far is:

ensembl67=useMart(host='may2012.archive.ensembl.org',
                  biomart='ENSEMBL_MART_ENSEMBL')
ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl67)

ADD COMMENTlink modified 8 weeks ago by Hervé Pagès ♦♦ 13k • written 8 weeks ago by Rob0
0
gravatar for Hervé Pagès
8 weeks ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi,

AFAIK SNP information for mouse can be found in different places via biomaRt:

1. In the snp_chromosome_strand attribute of the mmusculus_gene_ensembl dataset of the ENSEMBL_MART_ENSEMBL mart:

> library(biomaRt)
> mart <- useMart(host="may2012.archive.ensembl.org",
                  biomart="ENSEMBL_MART_ENSEMBL",
                  dataset="mmusculus_gene_ensembl")
> attribs <- listAttributes(mart)
> grep("snp", attribs$name, ignore.case=TRUE, value=TRUE)
[1] "snp_chromosome_strand"

2. In the mmusculus_snp and mmusculus_structvar datasets of the ENSEMBL_MART_SNP mart:

> listMarts(host="may2012.archive.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 67
2     ENSEMBL_MART_SNP  Ensembl Variation 67
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 67
4    ENSEMBL_MART_VEGA               Vega 47
5             REACTOME    REACTOME (CSHL US)
6                pride        PRIDE (EBI UK)

> snp_mart <- useMart(host="may2012.archive.ensembl.org",
                      biomart="ENSEMBL_MART_SNP")

> snp_datasets <- listDatasets(snp_mart)

> snp_datasets[grep("mus", snp_datasets$dataset), ]
               dataset                                           description
10       mmusculus_snp            Mus musculus Variation (dbSNP128; ENSEMBL)
11 mmusculus_structvar Mus musculus Structural Variation (dbSNP128; ENSEMBL)
             version
10 dbSNP128; ENSEMBL
11 dbSNP128; ENSEMBL

Hope this helps,

H.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Hervé Pagès ♦♦ 13k

That works great, thanks very much!

ADD REPLYlink written 8 weeks ago by Rob0
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