Galaxy | Published Workflow | PD GWAS Tutorial

Published Workflows | chris | PD GWAS Tutorial

Galaxy Workflow ' PD GWAS Tutorial'

Step	Annotation
Step 1: Input dataset input select at runtime
Step 2: snp2gcoords Input dataset Output dataset 'output' from step 1 CBM/Dintor release 2015-04 Input has header True Empty cell value -- Input ID column 1 Mapping data version v-00 Exclude SNPs that map to multiple locations True Include failed SNPs in the output False Include reference/alternate alleles and strand in the output True Add column with validation states False Restrict output to human chromosome names True
Step 3: Pos2LDBlock Input dataset Output dataset 'output' from step 2 CBM/Dintor release 2015-04 Input has header True Empty cell value -- Mapping data version v-00 Choose permissiveness option echo Column with genomic coordinates 2
Step 4: Interval2Genes Input dataset Output dataset 'output' from step 3 CBM/Dintor release 2015-04 Input has header True Empty cell value -- Mapping data version v-00 Choose permissiveness option echo Column with begin genomic coordinates 8 Column with end genomic coordinate 9 Variation genomic coordinate True Column with variation genomic coordinates 2
Step 5: HSGeneIdConverter Input dataset Output dataset 'output' from step 4 CBM/Dintor release 2015-04 Input has header True Empty cell value -- Choose permissiveness option echo Input ID column 10 Mapping data version v-00 Input ID Human Ensembl Gene ID Output ID HGNC Approved Symbol
Step 6: HSGeneOrthologyMapper Input dataset Output dataset 'output' from step 5 CBM/Dintor release 2015-04 Input has header True Empty cell value -- Choose permissiveness option echo Input ID column 10 Mapping data version v-00 Mapping type Human Ensembl Gene ID => Drosophila Ensembl Gene ID Include possible/putative orthologs in the output False Add column with type of homology True Add column with percentage identity with respect to the human gene True Add column with percentage identity with respect to the gene from the non-human organism True Add column with orthology confidence score False
Step 7: DMGeneIdConverter Input dataset Output dataset 'output' from step 6 CBM/Dintor release 2015-04 Input has header True Empty cell value -- Choose permissiveness option echo Input ID column 15 Mapping data version v-00 Input ID Drosophila Ensembl Gene ID Output ID FlyBase CG number
Step 8: DMGeneIdConverter Input dataset Output dataset 'output' from step 7 CBM/Dintor release 2015-04 Input has header True Empty cell value -- Choose permissiveness option echo Input ID column 15 Mapping data version v-00 Input ID Drosophila Ensembl Gene ID Output ID VDRC Transformant ID (r6.01)

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