Retrieve SNPs from regions around known genes

Created: 2007-11-07 15:50:40

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Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position)

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Option 1:

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http://myexperiment.org/workflows/70/download?version=1
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Workflow Components

Inputs (1)

Name	Description
GeneIDList	List of Ensemble gene identifiers for human.

Processors (6)

Name	Type	Description
Add1000	beanshell
ForceListType	local
NCBI36	biomart	Homo sapiens genes (NCBI36)
Subtract1000	beanshell
CreateReport	beanshell
dbSNP	biomart	Homo sapiens SNPs (dbSNP 125)

Beanshells (3)

Name	Inputs	Outputs
Add1000	input	output
Subtract1000	input	output
CreateReport	strand chromStart chrom snpID	result

Outputs (2)

Name	Description
ReportList
GeneIDList

Links (13)

Source	Sink
Add1000:output	dbSNP:hsapiens_snp.chrom_end_filter
GeneIDList	ForceListType:inputlist
CreateReport:result	ReportList
ForceListType:outputlist	GeneIDList
ForceListType:outputlist	NCBI36:hsapiens_gene_ensembl.gene_stable_id_filter
NCBI36:hsapiens_gene_ensembl.chromosome_name	dbSNP:hsapiens_snp.chr_name_filter
NCBI36:hsapiens_gene_ensembl.end_position	Add1000:input
NCBI36:hsapiens_gene_ensembl.start_position	Subtract1000:input
Subtract1000:output	dbSNP:hsapiens_snp.chrom_start_filter
dbSNP:hsapiens_snp.chr_name	CreateReport:chrom
dbSNP:hsapiens_snp.chrom_start	CreateReport:chromStart
dbSNP:hsapiens_snp.chrom_strand	CreateReport:strand
dbSNP:hsapiens_snp.refsnp_id	CreateReport:snpID