On Fri, Jan 29, 2010 at 2:02 PM, Dan Staines <[email protected]> wrote:
> So the SNP query you want is something like: >> >> >> http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.snp.ensembl_gene_id|hsapiens_gene_ensembl.default.snp.external_id|hsapiens_gene_ensembl.default.snp.synonymous_status|hsapiens_gene_ensembl.default.snp.snp_chromosome_strand|hsapiens_gene_ensembl.default.snp.chromosome_location&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id<http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.snp.ensembl_gene_id%7Chsapiens_gene_ensembl.default.snp.external_id%7Chsapiens_gene_ensembl.default.snp.synonymous_status%7Chsapiens_gene_ensembl.default.snp.snp_chromosome_strand%7Chsapiens_gene_ensembl.default.snp.chromosome_location&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id> >> < >> http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.snp.ensembl_gene_id|hsapiens_gene_ensembl.default.snp.external_id|hsapiens_gene_ensembl.default.snp.synonymous_status|hsapiens_gene_ensembl.default.snp.snp_chromosome_strand|hsapiens_gene_ensembl.default.snp.chromosome_location&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id<http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.snp.ensembl_gene_id%7Chsapiens_gene_ensembl.default.snp.external_id%7Chsapiens_gene_ensembl.default.snp.synonymous_status%7Chsapiens_gene_ensembl.default.snp.snp_chromosome_strand%7Chsapiens_gene_ensembl.default.snp.chromosome_location&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id> >> >."ENSG00000212912,ENSG00000000003,ENSG00000000005,ENSG00000000419,ENSG00000000457,ENSG00000000460,ENSG00000000938,ENSG00000000971,ENSG00000001036,ENSG00000001084,ENSG00000001167"|hsapiens_gene_ensembl.default.filters.snptype_filters."UPSTREAM"&VISIBLEPANEL=resultspanel >> >> >> But instead of pasting in the gene IDs you want this to be the result of >> another BioMart query, correct? Is the gene query one using the same >> ensembl genes dataset - if so you can just set the appropriate filters >> along with upstream snps only? If its a novel dataset of yours then you >> just need to set up dataset linking between human ensembl genes and your >> dataset on ensembl gene IDs. >> > > Thanks for the very helpful reply - I was forgetting upstream as a > consequence in this dataset, which doesn't help... Your suggestions comes > extremely close to fitting the bill and I could definitely use it as a > solution for the user (in the variation mart, rather than the main mart). > > However, lets suppose that the users wanted an upstream window 10kb or > other arbitrary figure (which is actually the original number I was given), > not the 5kb that the consequence represents. Beyond changing how the > consequence is created (or some other way of doing some precalculation to > populate the mart), could I do that? > At the moment the Ensembl marts won't let you do this. They would let you output a user defined length of upstream sequence for each gene but not the SNPs contained within these. At the moment the only way to achieve this would be to do the gene query and output gene start positions, use a script to convert those to the upstream region coordinates and feed those into a SNP mart query. Cheers Damian > > Cheers, > > > Dan. > > -- > Dan Staines, PhD Ensembl Genomes Technical Coordinator > EMBL-EBI Tel: +44-(0)1223-492507 > Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 > Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ >
