Broad Institute GDAC Firehose Standard Data Workflow Graph
Last Updated: 2014_05_03

This is the workflow graph for the GDAC Firehose stddata pipeline. A similar graph for Analyses pipeline executed upon these data is available here. This page was constructed with the help of GraphViz and PyDOT.


stddata CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_2__probeset_rma__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_3__unc_lowess_normalization_gene_level__data CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data Methylation_Preprocess Methylation_Preprocess Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data->Methylation_Preprocess mRNAseq_Preprocess mRNAseq_Preprocess mRNAseq_Preprocess->CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NT CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB mRNAseq_Preprocess->CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NB mRNAseq_Preprocess->Methylation_Preprocess CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB mRNAseq_Preprocess->CreateLoadfile_paradigm_mRNAseq_exp_RPKM_log2_NB CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT mRNAseq_Preprocess->CreateLoadfile_paradigm_mRNAseq_exp_RSEM_log2_NT Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data->CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NB mRNA_Preprocess_Median mRNA_Preprocess_Median Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data->mRNA_Preprocess_Median CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data->CreateLoadfile_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data_NT Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data->mRNAseq_Preprocess Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_loh__seg Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data->mRNAseq_Preprocess Merge_Clinical Merge_Clinical Clinical_Pick_Tier1 Clinical_Pick_Tier1 Merge_Clinical->Clinical_Pick_Tier1 Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg miRseq_Mature_Preprocess miRseq_Mature_Preprocess Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data->mRNAseq_Preprocess Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data Merge_exon__huex_1_0_st_v2__lbl_gov__Level_2__quantile_normalization_exon__data Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__exon_expression__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__junction_quantification__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__junction_quantification__data Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data->mRNAseq_Preprocess Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__exon_quantification__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__exon_quantification__data Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data Merge_mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data->mRNAseq_Preprocess Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_2__unc_lowess_normalization_probe_level__data CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data->CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NT Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data->mRNA_Preprocess_Median CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data->CreateLoadfile_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data_NB miRseq_Preprocess miRseq_Preprocess Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data Mutation_Packager_Calls Mutation_Packager_Calls Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_2__unc_lowess_normalization_probe_level__data Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data->mRNAseq_Preprocess Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cnv__seg Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg Merge_cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data->miRseq_Preprocess Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__splice_junction_expression__data Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data Merge_mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data->Methylation_Preprocess CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data->miRseq_Mature_Preprocess RPPA_AnnotateWithGene RPPA_AnnotateWithGene Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data->CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NT Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data->CreateLoadfile_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data_NB Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data->mRNA_Preprocess_Median mRNA_Preprocess_Median->Methylation_Preprocess Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg Mutation_Packager_Coverage Mutation_Packager_Coverage Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data->RPPA_AnnotateWithGene Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cnv__seg Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg Merge_snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg Merge_cna__cgh_1x1m_g4447a__mskcc_org__Level_3__segmentation_data_computation__seg Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg Merge_snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg Merge_cna__hg_cgh_244a__hms_harvard_edu__Level_3__segmentation__seg Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg Merge_cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data->mRNAseq_Preprocess Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data Merge_transcriptome__agilentg4502a_07_1__unc_edu__Level_2__unc_lowess_normalization_probe_level__data Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data->miRseq_Preprocess



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This page generated on: Tue Nov 22 09:21:16 EST 2016