/groups/umcg-bios/
|-- prm02
|   |-- projects
|   |   |-- annotations
|   |   |-- eQTLmapping
|   |   |   |-- BIOS
|   |   |   |   |-- exon_level
|   |   |   |   `-- gene_level
|   |   |   |-- Geuvadis
|   |   |   |   |-- gene_level
|   |   |   |   |   |-- eQTLs_meta_20PCs
|   |   |   |   |   |   `-- old_wrong_gte
|   |   |   |   |   |       |-- plots
|   |   |   |   |   |       `-- plots_opposite_effects_replication_bbmri
|   |   |   |   |   |           `-- plots [error opening dir]
|   |   |   |   |   |-- eQTLs_meta_20PCs_replication_bbmri_genelevel
|   |   |   |   |   |   `-- old_wrong_gte
|   |   |   |   |   |-- eQTLs_meta_20PCs_secondary_effects
|   |   |   |   |   |   |-- distance_to_TSS
|   |   |   |   |   |   |-- expressionWithPrimaryEffectsRegressedOut
|   |   |   |   |   |   |-- geuvadis_eQTLs_meta_20PCs_1-0_RegressedOut_15012015
|   |   |   |   |   |   |-- geuvadis_eQTLs_meta_20PCs_1-1_RegressedOut_15012015
|   |   |   |   |   |   |-- geuvadis_eQTLs_meta_20PCs_1-2_RegressedOut_15012015
|   |   |   |   |   |   |-- geuvadis_eQTLs_meta_20PCs_1-3_RegressedOut_15012015
|   |   |   |   |   |   `-- geuvadis_eQTLs_meta_20PCs_1-4_RegressedOut_15012015
|   |   |   |   |   `-- replicationOfBiosAllLevels
|   |   |   |   `-- meta-exon_level
|   |   |   |       |-- eQTLs_meta_20PCs
|   |   |   |       |   `-- old_gte
|   |   |   |       `-- eQTLs_meta_20PCs_bbmri_replication
|   |   |   |           `-- old_gtes
|   |   |   |-- geuvadis_gene_replication_in_bbmri_oldGte
|   |   |   `-- GoShifter_annotation
|   |   |       |-- compute-pipeline
|   |   |       |   |-- protocols
|   |   |       |   `-- templates
|   |   |       `-- LL+RS+CODAM+LLS_eqtls_genes_23062014
|   |   |           |-- differenceGeuvadis
|   |   |           |   |-- BIOS-Geuvadis
|   |   |           |   |   |-- notReplicated
|   |   |           |   |   |   |-- goshifter_output [error opening dir]
|   |   |           |   |   |   `-- scripts
|   |   |           |   |   |-- replicatedOpposite
|   |   |           |   |   |   |-- goshifter_output [error opening dir]
|   |   |           |   |   |   `-- scripts
|   |   |           |   |   `-- replicatedSame
|   |   |           |   |       |-- goshifter_output [error opening dir]
|   |   |           |   |       `-- scripts
|   |   |           |   |-- notReplicated
|   |   |           |   |   |-- goshifter_output [error opening dir]
|   |   |           |   |   `-- scripts
|   |   |           |   |-- replicatedOpposite
|   |   |           |   |   |-- goshifter_output [error opening dir]
|   |   |           |   |   `-- scripts
|   |   |           |   `-- replicatedSame
|   |   |           |       |-- goshifter_output [error opening dir]
|   |   |           |       `-- scripts
|   |   |           |-- goshifter_output [error opening dir]
|   |   |           `-- LD
|   |   |-- expression
|   |   |   |-- BBMRI+Geuvadis_joint_normalization
|   |   |   |-- gene_level_additional
|   |   |   |-- Geuvadis
|   |   |   |   |-- EUR+YRI
|   |   |   |   |   `-- EUR+YRI_eQTLs_meta_25PCs
|   |   |   |   |-- gene_level
|   |   |   |   |-- interactionAnalysis
|   |   |   |   |-- meta-exon_level
|   |   |   |   `-- TriTyper
|   |   |   |       |-- CEU
|   |   |   |       |   `-- CEU.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed
|   |   |   |       |-- FIN
|   |   |   |       |   `-- FIN.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed
|   |   |   |       |-- GBR
|   |   |   |       |   `-- GBR.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed
|   |   |   |       `-- TSI
|   |   |   |           `-- TSI.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed
|   |   |   |-- meta-exon_level_additional
|   |   |   |-- per_cohort
|   |   |   |   `-- LL
|   |   |   `-- transcript_level_additional
|   |   |-- genotypes
|   |   |   |-- CODAM-imputed-20140306-TriTyper
|   |   |   |-- LL-imputed-20140306-TriTyper
|   |   |   |-- LLS-imputed-20140402-TriTyper
|   |   |   |-- NTR_AC-imputed-20140606-TriTyper
|   |   |   |-- NTR_Aff6-imputed-20140606-TriTyper
|   |   |   |-- PAN-imputed-20140306-TriTyper
|   |   |   |-- RNAseq_genotypes
|   |   |   |   |-- CODAM_SNVMix_TriTyper
|   |   |   |   |-- LL_SNVMix_TriTyper
|   |   |   |   `-- RS_SNVMix_TriTyper
|   |   |   `-- RS-imputed-20140306-TriTyper
|   |   |-- imputed
|   |   |   |-- CODAM
|   |   |   |   |-- genotypes
|   |   |   |   |   |-- b36
|   |   |   |   |   |-- b37
|   |   |   |   |   |   |-- old
|   |   |   |   |   |   `-- qc
|   |   |   |   |   `-- rawdata
|   |   |   |   `-- jobs
|   |   |   |-- NTR
|   |   |   |   |-- genotypes
|   |   |   |   |   |-- NTR_B37_AC_Epigen_CAUT
|   |   |   |   |   |   |-- b37
|   |   |   |   |   |   |   `-- backup
|   |   |   |   |   |   `-- rawdata
|   |   |   |   |   |-- NTR_B37_AC_Epigen_CX
|   |   |   |   |   |   `-- rawdata
|   |   |   |   |   `-- NTR_B37_Aff6_Epigen
|   |   |   |   |       |-- b37
|   |   |   |   |       |   `-- backup
|   |   |   |   |       `-- rawdata
|   |   |   |   `-- jobs
|   |   |   |-- PAN
|   |   |   |   |-- genotypes
|   |   |   |   |   |-- b37
|   |   |   |   |   |   |-- original
|   |   |   |   |   |   `-- qc
|   |   |   |   |   `-- rawdata
|   |   |   |   `-- jobs
|   |   |   `-- RS
|   |   |       |-- genotypes
|   |   |       |   |-- b36
|   |   |       |   |-- b37
|   |   |       |   `-- rawdata
|   |   |       `-- jobs
|   |   |-- interactionAnalysis
|   |   |   |-- BIOS
|   |   |   |   |-- biosInteractions8
|   |   |   |   |-- eQTLs_all_levels
|   |   |   |   `-- GWAS_eQTLs
|   |   |   |       |-- Body_mass_index
|   |   |   |       |-- Bone_mineral_density
|   |   |   |       |-- Celiac_disease
|   |   |   |       |-- Crohns_disease
|   |   |   |       |-- HDL_cholesterol
|   |   |   |       |-- Height
|   |   |   |       |-- Inflammatory_bowel_disease
|   |   |   |       |-- LDL_cholesterol
|   |   |   |       |-- Mean_platelet_volume
|   |   |   |       |-- Metabolic_traits
|   |   |   |       |-- Metabolite_levels
|   |   |   |       |-- Multiple_sclerosis
|   |   |   |       |-- Platelet_counts
|   |   |   |       |-- Prostate_cancer
|   |   |   |       |-- Psoriasis
|   |   |   |       |-- Red_blood_cell_traits
|   |   |   |       |-- Rheumatoid_arthritis
|   |   |   |       |-- Schizophrenia
|   |   |   |       |-- Total_cholesterol
|   |   |   |       |-- Triglycerides
|   |   |   |       |-- Type_1_diabetes
|   |   |   |       `-- Ulcerative_colitis
|   |   |   `-- Geuvadis
|   |   `-- oldImputations
|   |       |-- CODAM
|   |       |   `-- imputedGenotypeData
|   |       |-- LLS
|   |       |   `-- chunks
|   |       `-- Rotterdam
|   |           |-- Aligend
|   |           |-- imputation
|   |           |-- imputationTriTyper
|   |           |-- imputed
|   |           |-- mergedRs
|   |           |-- mergedRs1Rs2
|   |           |-- mergedRs1Rs2AligedToRs3
|   |           |-- phasing
|   |           |   `-- generatedScripts
|   |           |-- rs1
|   |           |-- rs2
|   |           `-- rs3
|   `-- rawdata
|       `-- rnaseq
|-- scr01 -> /local/groups/umcg-bios/scr01
|-- scr02 -> /local2/groups/umcg-bios/scr02
`-- tmp04
    |-- projects
    |   |-- bbmriSampleInfo
    |   |   `-- v2.1.1
    |   |-- biosDatabase
    |   |-- BIOS_RNA
    |   |   |-- batch0
    |   |   |   |-- jobs
    |   |   |   |   |-- genotypeCalling
    |   |   |   |   |-- QC
    |   |   |   |   `-- quantification
    |   |   |   `-- results
    |   |   |       |-- addOrReplaceReadGroups
    |   |   |       |-- baseQualityScoreRecalibration
    |   |   |       |-- collectMultipleMetrics_genotypeCalling
    |   |   |       |-- collectMultipleMetrics_QC
    |   |   |       |-- collectRnaSeqMetrics_genotypeCalling
    |   |   |       |-- collectRnaSeqMetrics_QC
    |   |   |       |-- covariateAnalysis
    |   |   |       |-- fastqc
    |   |   |       |-- filteredBam
    |   |   |       |-- flagStat
    |   |   |       |-- genotypeHarmonizer
    |   |   |       |-- haplotypeCaller
    |   |   |       |-- hisat
    |   |   |       |-- indelRealignment
    |   |   |       |-- kallisto
    |   |   |       |-- markDuplicates
    |   |   |       |-- mergeBams
    |   |   |       |-- sortedBam
    |   |   |       |-- splitAndTrim
    |   |   |       |-- unfilteredBam
    |   |   |       |-- unifiedGenotype
    |   |   |       |-- variantEval
    |   |   |       `-- verifyBamID
    |   |   `-- batch1
    |   |       |-- jobs
    |   |       |   |-- QC
    |   |       |   `-- quantification
    |   |       `-- results
    |   |           |-- collectMultipleMetrics_QC
    |   |           |-- collectRnaSeqMetrics_QC
    |   |           |-- fastqc
    |   |           |-- filteredBam
    |   |           |-- genotypeHarmonizer
    |   |           |-- hisat
    |   |           |-- kallisto
    |   |           |-- sortedBam
    |   |           |-- unfilteredBam
    |   |           |-- unifiedGenotype
    |   |           |-- variantEval
    |   |           `-- verifyBamID
    |   `-- genotypes
    |       |-- CODAM-imputed-20140306-TriTyper
    |       |-- LL-imputed-20140306-TriTyper
    |       |-- LLS-imputed-20140402-TriTyper
    |       |-- NTR_AC-imputed-20140606-TriTyper
    |       |-- NTR_Aff6-imputed-20140606-TriTyper
    |       |-- PAN-imputed-20140306-TriTyper
    |       |-- RNAseq_genotypes
    |       |   |-- CODAM_SNVMix_TriTyper
    |       |   |-- LL_SNVMix_TriTyper
    |       |   `-- RS_SNVMix_TriTyper
    |       `-- RS-imputed-20140306-TriTyper
    |-- rawdata
    |   `-- rnaseq
    `-- users
        |-- umcg-aclaringbould
        |   |-- abun1
        |   |-- abun2
        |   |-- abun3
        |   |-- bbmri_duplicates
        |   |-- eQTLpipeline
        |   |   |-- backup
        |   |   |-- cis
        |   |   |-- first_norm
        |   |   `-- mixupmapping
        |   |       |-- Cis-eQTLs
        |   |       |-- CODAM
        |   |       |   |-- Cis-eQTLs
        |   |       |   `-- MixupMapper
        |   |       |-- LL
        |   |       |   |-- Cis-eQTLs
        |   |       |   `-- MixupMapper
        |   |       |-- LLS
        |   |       |   |-- Cis-eQTLs
        |   |       |   `-- MixupMapper
        |   |       |-- NTR_AC
        |   |       |   |-- Cis-eQTLs
        |   |       |   `-- MixupMapper
        |   |       |-- NTR_Aff6
        |   |       |-- PAN
        |   |       |   |-- Cis-eQTLs
        |   |       |   `-- MixupMapper
        |   |       `-- RS
        |   |           |-- Cis-eQTLs
        |   |           `-- MixupMapper
        |   `-- scripts
        `-- umcg-ndeklein
            `-- samplesheets

277 directories