myExperiment.org - Workflows - Retrieve SNPs from regions around known genes (Alan Williams) [Taverna 1 Workflow]

Workflow Entry: Retrieve SNPs from regions around known genes

Created at: 05/03/08 @ 14:12:33 Last updated: 29/07/08 @ 15:18:38

Version 1 (of 1)

Version created on: 05/03/08 @ 14:12:32 by: Alan Williams | Revision comments Expand

Last edited on: 29/07/08 @ 15:18:38 by: Alan Williams

Title: Retrieve SNPs from regions around known genes

Type: Taverna 1

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Description

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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Workflow Components

Inputs (1)

Name	Description
GeneIDList	List of Ensemble gene identifiers for human. For example ENSG00000205607

Processors (6)

Name	Type	Description
Add1000	beanshell
Subtract1000	beanshell
CreateReport	beanshell
ForceListType	local
NCBI36	biomart	Homo sapiens genes (NCBI36)
dbSNP	biomart	Homo sapiens SNPs (dbSNP 126; HGVbase 15; TSC 1; affy GeneChip Mapping Array)

Outputs (2)

Name	Description
ReportList
GeneIDList

Links (13)

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

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Taverna 1 workflow

Information Original Uploader

Alan Williams

Information License

All versions of this Workflow are licensed under the Creative Commons Attribution 3.0 License.

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Tomoinn

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Taverna workflow workbench examples

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Information Favourited By (1)

David De Roure

Information Statistics

496 viewings

375 downloads

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Version History

Earliest Version:
[1] - Retrieve SNPs from regions around known genes

Created on: Wednesday 05 March 2008 @ 14:12:32 (GMT)

Created by: Alan Williams

Last edited on: Tuesday 29 July 2008 @ 15:18:38 (BST)

Last edited by: Alan Williams

Revision comments:

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This Workflow only has one version.

Comments (2)

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Alan Williams	Friday 10 October 2008 @ 11:15:10 (BST)
	There is a problem with the suggested example input. The workflow should run OK with other geneIDs. Note that depending upon the ID it may take a long time.

Paolo

this runs quickly (a few secs) in T2 with each of these two inputs:

ENSG00000083093

ENSG00000139618

but I couldn't get it to take a _list_ with these two inputs

T2 seems to believe the input is a string, not a list. T1 takes a list as expected

Workflow Entry: Retrieve SNPs from regions around known genes

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