Search
Question: biomaRt: SNP no access to grch37.ensembl.org
0
gravatar for mrprao
2.7 years ago by
mrprao0
United States
mrprao0 wrote:

Hi,

How do I access the SNPs (say rs ids to coordinates)  from this GRCH37 archive  http://grch37.ensembl.org archive.

useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="?????")

>snp_mart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="SNP")
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) :
  The given dataset:  SNP , is not valid.  Correct dataset names can be obtained with the listDatasets function.
Calls: useMart -> useDataset
>
> snp_mart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_snp_ensembl")
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) :
  The given dataset:  hsapiens_snp_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
Calls: useMart -> useDataset

> listDatasets(useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice"))                                                                                                    
                          dataset                                 description                                                                                                                                      
                                                                                                                                 
31          hsapiens_gene_ensembl             Homo sapiens genes (GRCh37.p13)                                                                                                                                      
                                                                                                                                                                                                                                                          
           version                                                                                                                                                                                                 

31      GRCh37.p13

>

There is no SNP dataset either

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by mrprao0
0
gravatar for Thomas Maurel
2.7 years ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:
You can get the list of the available GRCh37 marts by running the following command: > listMarts(host='grch37.ensembl.org') biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 2 ENSEMBL_MART_SNP Ensembl Variation 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 4 ENSEMBL_MART_VEGA Vega 5 pride PRIDE (EBI UK) The following command will give you the list of datasets available for the GRCh37 snp mart: > grch37_snp = useMart(biomart="ENSEMBL_MART_SNP", host="grch37.ensembl.org") > listDatasets(grch37_snp) dataset description version 1 ecaballus_snp Equus caballus Short Variation (SNPs and indels) (EquCab2) EquCab2 2 hsapiens_snp Homo sapiens Short Variation (SNPs and indels) (GRCh37.p13) GRCh37.p13 3 hsapiens_structvar Homo sapiens Structural Variation (GRCh37.p13) GRCh37.p13 4 oanatinus_snp Ornithorhynchus anatinus Short Variation (SNPs and indels) (OANA5) OANA5 5 tnigroviridis_snp Tetraodon nigroviridis Short Variation (SNPs and indels) (TETRAODON8.0) TETRAODON8.0 6 oaries_snp Ovis Aries Short Variation (SNPs and indels) (Oar_v3.1) Oar_v3.1 7 drerio_snp Danio rerio Short Variation (SNPs and indels) (Zv9) Zv9 8 mdomestica_snp Monodelphis domestica Short Variation (SNPs and indels) (monDom5) monDom5 9 cfamiliaris_structvar Canis familiaris Structural Variation (CanFam3.1) CanFam3.1 10 btaurus_snp Bos taurus Short Variation (SNPs and indels) (UMD3.1) UMD3.1 11 mmulatta_snp Macaca mulatta Short Variation (SNPs and indels) (MMUL_1) MMUL_1 12 nleucogenys_snp Nomascus leucogenys Short Variation (SNPs and indels) (Nleu1.0) Nleu1.0 13 mgallopavo_snp Meleagris gallopavo Short Variation (SNPs and indels) (UMD2) UMD2 14 ecaballus_structvar Equus caballus Structural Variation (EquCab2) EquCab2 15 tguttata_snp Taeniopygia guttata Short Variation (SNPs and indels) (taeGut3.2.4) taeGut3.2.4 16 fcatus_snp Felis catus Short Variation (SNPs and indels) (Felis_catus_6.2) Felis_catus_6.2 17 hsapiens_structvar_som Homo sapiens Somatic Structural Variation (GRCh37.p13) GRCh37.p13 18 dmelanogaster_snp Drosophila melanogaster Short Variation (SNPs and indels) (BDGP5) BDGP5 19 rnorvegicus_snp Rattus norvegicus Short Variation (SNPs and indels) (Rnor_5.0) Rnor_5.0 20 pabelii_snp Pongo abelii Short Variation (SNPs and indels) (PPYG2) PPYG2 21 ggallus_snp Gallus gallus Short Variation (SNPs and indels) (Galgal4) Galgal4 22 scerevisiae_snp Saccharomyces cerevisiae Short Variation (SNPs and indels) (R64-1-1) R64-1-1 23 drerio_structvar Danio rerio Structural Variation (Zv9) Zv9 24 mmulatta_structvar Macaca mulatta Structural Variation (MMUL_1) MMUL_1 25 mmusculus_snp Mus musculus Short Variation (SNPs and indels) (GRCm38.p2) GRCm38.p2 26 mmusculus_structvar Mus musculus Structural Variation (GRCm38.p2) GRCm38.p2 27 btaurus_structvar Bos taurus Structural Variation (UMD3.1) UMD3.1 28 ptroglodytes_snp Pan troglodytes Short Variation (SNPs and indels) (CHIMP2.1.4) CHIMP2.1.4 29 sscrofa_structvar Sus scrofa Structural Variation (Sscrofa10.2) Sscrofa10.2 30 hsapiens_snp_som Homo sapiens Somatic Short Variation (SNPs and indels) (GRCh37.p13) GRCh37.p13 31 cfamiliaris_snp Canis familiaris Short Variation (SNPs and indels) (CanFam3.1) CanFam3.1 32 sscrofa_snp Sus scrofa Short Variation (SNPs and indels) (Sscrofa10.2) Sscrofa10.2 To query human GRCh37 snp mart, you can just use one of the following command: 1) For germline data: grch37_snp = useMart(biomart=“ENSEMBL_MART_SNP", host="grch37.ensembl.org", dataset="hsapiens_snp") 2) For the somatic data: grch37_snp_som = useMart(biomart=“ENSEMBL_MART_SNP", host="grch37.ensembl.org", dataset="hsapiens_snp_som") 3) For the structural variation germline data: grch37_structvar = useMart(biomart=“ENSEMBL_MART_SNP”, host="grch37.ensembl.org", dataset="hsapiens_structvar") 4) For the structural variation somatic data: grch37_structvar_som = useMart(biomart=“ENSEMBL_MART_SNP”, host="grch37.ensembl.org", dataset="hsapiens_structvar_som") Hope this helps, Thomas > On 19 Mar 2015, at 19:26, mrprao [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org <https: support.bioconductor.org=""/> > User mrprao <https: support.bioconductor.org="" u="" 7486=""/> wrote Question: biomaRt: SNP no access to grch37.ensembl.org <https: support.bioconductor.org="" p="" 65831=""/>: > > > Hi, > > How do I access the SNPs (say rs ids to coordinates) from this GRCH37 archive http://grch37.ensembl.org <http: grch37.ensembl.org=""/> archive. > > useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="?????") > >snp_mart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="SNP") > Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : > The given dataset: SNP , is not valid. Correct dataset names can be obtained with the listDatasets function. > Calls: useMart -> useDataset > > > > snp_mart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_snp_ensembl") > Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : > The given dataset: hsapiens_snp_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function. > Calls: useMart -> useDataset > > > listDatasets(useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice")) > dataset description > > 31 hsapiens_gene_ensembl Homo sapiens genes (GRCh37.p13) > > version > > 31 GRCh37.p13 > > > > > There is no SNP dataset either > > > You may reply via email or visit biomaRt: SNP no access to grch37.ensembl.org > -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom
ADD COMMENTlink written 2.7 years ago by Thomas Maurel700
0
gravatar for mrprao
2.7 years ago by
mrprao0
United States
mrprao0 wrote:

Thank TM, Got it worked

(solution for others )

# GRCH37 ensemble SNP

snp_mart = useMart(biomart="ENSEMBL_MART_SNP", host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_snp")

RSids = c("rs16828074", "rs17232800")

snp_attributes = c("refsnp_id", "chr_name", "chrom_start")

snp_locations = getBM(attributes=snp_attributes, filters="snp_filter",
                      values=RSids, mart=snp_mart)

head(snp_locations)

 

ADD COMMENTlink written 2.7 years ago by mrprao0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 101 users visited in the last hour