| 1 | /groups/umcg-bios/ |
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| 2 | |-- prm02 |
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| 3 | | |-- projects |
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| 4 | | | |-- annotations |
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| 5 | | | |-- eQTLmapping |
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| 6 | | | | |-- BIOS |
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| 7 | | | | | |-- exon_level |
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| 8 | | | | | `-- gene_level |
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| 9 | | | | |-- Geuvadis |
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| 10 | | | | | |-- gene_level |
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| 11 | | | | | | |-- eQTLs_meta_20PCs |
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| 12 | | | | | | | `-- old_wrong_gte |
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| 13 | | | | | | | |-- plots |
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| 14 | | | | | | | `-- plots_opposite_effects_replication_bbmri |
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| 15 | | | | | | | `-- plots [error opening dir] |
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| 16 | | | | | | |-- eQTLs_meta_20PCs_replication_bbmri_genelevel |
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| 17 | | | | | | | `-- old_wrong_gte |
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| 18 | | | | | | |-- eQTLs_meta_20PCs_secondary_effects |
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| 19 | | | | | | | |-- distance_to_TSS |
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| 20 | | | | | | | |-- expressionWithPrimaryEffectsRegressedOut |
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| 21 | | | | | | | |-- geuvadis_eQTLs_meta_20PCs_1-0_RegressedOut_15012015 |
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| 22 | | | | | | | |-- geuvadis_eQTLs_meta_20PCs_1-1_RegressedOut_15012015 |
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| 23 | | | | | | | |-- geuvadis_eQTLs_meta_20PCs_1-2_RegressedOut_15012015 |
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| 24 | | | | | | | |-- geuvadis_eQTLs_meta_20PCs_1-3_RegressedOut_15012015 |
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| 25 | | | | | | | `-- geuvadis_eQTLs_meta_20PCs_1-4_RegressedOut_15012015 |
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| 26 | | | | | | `-- replicationOfBiosAllLevels |
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| 27 | | | | | `-- meta-exon_level |
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| 28 | | | | | |-- eQTLs_meta_20PCs |
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| 29 | | | | | | `-- old_gte |
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| 30 | | | | | `-- eQTLs_meta_20PCs_bbmri_replication |
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| 31 | | | | | `-- old_gtes |
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| 32 | | | | |-- geuvadis_gene_replication_in_bbmri_oldGte |
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| 33 | | | | `-- GoShifter_annotation |
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| 34 | | | | |-- compute-pipeline |
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| 35 | | | | | |-- protocols |
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| 36 | | | | | `-- templates |
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| 37 | | | | `-- LL+RS+CODAM+LLS_eqtls_genes_23062014 |
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| 38 | | | | |-- differenceGeuvadis |
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| 39 | | | | | |-- BIOS-Geuvadis |
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| 40 | | | | | | |-- notReplicated |
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| 41 | | | | | | | |-- goshifter_output [error opening dir] |
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| 42 | | | | | | | `-- scripts |
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| 43 | | | | | | |-- replicatedOpposite |
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| 44 | | | | | | | |-- goshifter_output [error opening dir] |
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| 45 | | | | | | | `-- scripts |
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| 46 | | | | | | `-- replicatedSame |
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| 47 | | | | | | |-- goshifter_output [error opening dir] |
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| 48 | | | | | | `-- scripts |
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| 49 | | | | | |-- notReplicated |
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| 50 | | | | | | |-- goshifter_output [error opening dir] |
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| 51 | | | | | | `-- scripts |
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| 52 | | | | | |-- replicatedOpposite |
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| 53 | | | | | | |-- goshifter_output [error opening dir] |
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| 54 | | | | | | `-- scripts |
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| 55 | | | | | `-- replicatedSame |
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| 56 | | | | | |-- goshifter_output [error opening dir] |
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| 57 | | | | | `-- scripts |
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| 58 | | | | |-- goshifter_output [error opening dir] |
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| 59 | | | | `-- LD |
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| 60 | | | |-- expression |
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| 61 | | | | |-- BBMRI+Geuvadis_joint_normalization |
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| 62 | | | | |-- gene_level_additional |
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| 63 | | | | |-- Geuvadis |
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| 64 | | | | | |-- EUR+YRI |
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| 65 | | | | | | `-- EUR+YRI_eQTLs_meta_25PCs |
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| 66 | | | | | |-- gene_level |
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| 67 | | | | | |-- interactionAnalysis |
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| 68 | | | | | |-- meta-exon_level |
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| 69 | | | | | `-- TriTyper |
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| 70 | | | | | |-- CEU |
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| 71 | | | | | | `-- CEU.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed |
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| 72 | | | | | |-- FIN |
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| 73 | | | | | | `-- FIN.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed |
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| 74 | | | | | |-- GBR |
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| 75 | | | | | | `-- GBR.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed |
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| 76 | | | | | `-- TSI |
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| 77 | | | | | `-- TSI.TMM.ProbesWithZeroVarianceRemoved.Log2Transformed.ProbesCentered.SamplesZTransformed |
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| 78 | | | | |-- meta-exon_level_additional |
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| 79 | | | | |-- per_cohort |
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| 80 | | | | | `-- LL |
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| 81 | | | | `-- transcript_level_additional |
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| 82 | | | |-- genotypes |
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| 83 | | | | |-- CODAM-imputed-20140306-TriTyper |
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| 84 | | | | |-- LL-imputed-20140306-TriTyper |
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| 85 | | | | |-- LLS-imputed-20140402-TriTyper |
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| 86 | | | | |-- NTR_AC-imputed-20140606-TriTyper |
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| 87 | | | | |-- NTR_Aff6-imputed-20140606-TriTyper |
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| 88 | | | | |-- PAN-imputed-20140306-TriTyper |
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| 89 | | | | |-- RNAseq_genotypes |
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| 90 | | | | | |-- CODAM_SNVMix_TriTyper |
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| 91 | | | | | |-- LL_SNVMix_TriTyper |
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| 92 | | | | | `-- RS_SNVMix_TriTyper |
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| 93 | | | | `-- RS-imputed-20140306-TriTyper |
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| 94 | | | |-- imputed |
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| 95 | | | | |-- CODAM |
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| 96 | | | | | |-- genotypes |
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| 97 | | | | | | |-- b36 |
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| 98 | | | | | | |-- b37 |
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| 99 | | | | | | | |-- old |
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| 100 | | | | | | | `-- qc |
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| 101 | | | | | | `-- rawdata |
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| 102 | | | | | `-- jobs |
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| 103 | | | | |-- NTR |
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| 104 | | | | | |-- genotypes |
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| 105 | | | | | | |-- NTR_B37_AC_Epigen_CAUT |
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| 106 | | | | | | | |-- b37 |
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| 107 | | | | | | | | `-- backup |
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| 108 | | | | | | | `-- rawdata |
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| 109 | | | | | | |-- NTR_B37_AC_Epigen_CX |
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| 110 | | | | | | | `-- rawdata |
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| 111 | | | | | | `-- NTR_B37_Aff6_Epigen |
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| 112 | | | | | | |-- b37 |
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| 113 | | | | | | | `-- backup |
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| 114 | | | | | | `-- rawdata |
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| 115 | | | | | `-- jobs |
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| 116 | | | | |-- PAN |
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| 117 | | | | | |-- genotypes |
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| 118 | | | | | | |-- b37 |
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| 119 | | | | | | | |-- original |
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| 120 | | | | | | | `-- qc |
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| 121 | | | | | | `-- rawdata |
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| 122 | | | | | `-- jobs |
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| 123 | | | | `-- RS |
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| 124 | | | | |-- genotypes |
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| 125 | | | | | |-- b36 |
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| 126 | | | | | |-- b37 |
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| 127 | | | | | `-- rawdata |
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| 128 | | | | `-- jobs |
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| 129 | | | |-- interactionAnalysis |
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| 130 | | | | |-- BIOS |
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| 131 | | | | | |-- biosInteractions8 |
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| 132 | | | | | |-- eQTLs_all_levels |
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| 133 | | | | | `-- GWAS_eQTLs |
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| 134 | | | | | |-- Body_mass_index |
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| 135 | | | | | |-- Bone_mineral_density |
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| 136 | | | | | |-- Celiac_disease |
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| 137 | | | | | |-- Crohns_disease |
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| 138 | | | | | |-- HDL_cholesterol |
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| 139 | | | | | |-- Height |
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| 140 | | | | | |-- Inflammatory_bowel_disease |
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| 141 | | | | | |-- LDL_cholesterol |
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| 142 | | | | | |-- Mean_platelet_volume |
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| 143 | | | | | |-- Metabolic_traits |
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| 144 | | | | | |-- Metabolite_levels |
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| 145 | | | | | |-- Multiple_sclerosis |
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| 146 | | | | | |-- Platelet_counts |
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| 147 | | | | | |-- Prostate_cancer |
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| 148 | | | | | |-- Psoriasis |
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| 149 | | | | | |-- Red_blood_cell_traits |
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| 150 | | | | | |-- Rheumatoid_arthritis |
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| 151 | | | | | |-- Schizophrenia |
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| 152 | | | | | |-- Total_cholesterol |
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| 153 | | | | | |-- Triglycerides |
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| 154 | | | | | |-- Type_1_diabetes |
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| 155 | | | | | `-- Ulcerative_colitis |
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| 156 | | | | `-- Geuvadis |
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| 157 | | | `-- oldImputations |
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| 158 | | | |-- CODAM |
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| 159 | | | | `-- imputedGenotypeData |
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| 160 | | | |-- LLS |
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| 161 | | | | `-- chunks |
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| 162 | | | `-- Rotterdam |
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| 163 | | | |-- Aligend |
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| 164 | | | |-- imputation |
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| 165 | | | |-- imputationTriTyper |
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| 166 | | | |-- imputed |
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| 167 | | | |-- mergedRs |
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| 168 | | | |-- mergedRs1Rs2 |
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| 169 | | | |-- mergedRs1Rs2AligedToRs3 |
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| 170 | | | |-- phasing |
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| 171 | | | | `-- generatedScripts |
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| 172 | | | |-- rs1 |
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| 173 | | | |-- rs2 |
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| 174 | | | `-- rs3 |
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| 175 | | `-- rawdata |
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| 176 | | `-- rnaseq |
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| 177 | |-- scr01 -> /local/groups/umcg-bios/scr01 |
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| 178 | |-- scr02 -> /local2/groups/umcg-bios/scr02 |
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| 179 | `-- tmp04 |
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| 180 | |-- projects |
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| 181 | | |-- bbmriSampleInfo |
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| 182 | | | `-- v2.1.1 |
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| 183 | | |-- biosDatabase |
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| 184 | | |-- BIOS_RNA |
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| 185 | | | |-- batch0 |
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| 186 | | | | |-- jobs |
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| 187 | | | | | |-- genotypeCalling |
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| 188 | | | | | |-- QC |
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| 189 | | | | | `-- quantification |
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| 190 | | | | `-- results |
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| 191 | | | | |-- addOrReplaceReadGroups |
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| 192 | | | | |-- baseQualityScoreRecalibration |
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| 193 | | | | |-- collectMultipleMetrics_genotypeCalling |
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| 194 | | | | |-- collectMultipleMetrics_QC |
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| 195 | | | | |-- collectRnaSeqMetrics_genotypeCalling |
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| 196 | | | | |-- collectRnaSeqMetrics_QC |
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| 197 | | | | |-- covariateAnalysis |
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| 198 | | | | |-- fastqc |
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| 199 | | | | |-- filteredBam |
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| 200 | | | | |-- flagStat |
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| 201 | | | | |-- genotypeHarmonizer |
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| 202 | | | | |-- haplotypeCaller |
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| 203 | | | | |-- hisat |
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| 204 | | | | |-- indelRealignment |
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| 205 | | | | |-- kallisto |
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| 206 | | | | |-- markDuplicates |
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| 207 | | | | |-- mergeBams |
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| 208 | | | | |-- sortedBam |
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| 209 | | | | |-- splitAndTrim |
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| 210 | | | | |-- unfilteredBam |
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| 211 | | | | |-- unifiedGenotype |
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| 212 | | | | |-- variantEval |
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| 213 | | | | `-- verifyBamID |
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| 214 | | | `-- batch1 |
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| 215 | | | |-- jobs |
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| 216 | | | | |-- QC |
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| 217 | | | | `-- quantification |
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| 218 | | | `-- results |
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| 219 | | | |-- collectMultipleMetrics_QC |
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| 220 | | | |-- collectRnaSeqMetrics_QC |
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| 221 | | | |-- fastqc |
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| 222 | | | |-- filteredBam |
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| 223 | | | |-- genotypeHarmonizer |
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| 224 | | | |-- hisat |
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| 225 | | | |-- kallisto |
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| 226 | | | |-- sortedBam |
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| 227 | | | |-- unfilteredBam |
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| 228 | | | |-- unifiedGenotype |
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| 229 | | | |-- variantEval |
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| 230 | | | `-- verifyBamID |
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| 231 | | `-- genotypes |
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| 232 | | |-- CODAM-imputed-20140306-TriTyper |
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| 233 | | |-- LL-imputed-20140306-TriTyper |
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| 234 | | |-- LLS-imputed-20140402-TriTyper |
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| 235 | | |-- NTR_AC-imputed-20140606-TriTyper |
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| 236 | | |-- NTR_Aff6-imputed-20140606-TriTyper |
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| 237 | | |-- PAN-imputed-20140306-TriTyper |
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| 238 | | |-- RNAseq_genotypes |
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| 239 | | | |-- CODAM_SNVMix_TriTyper |
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| 240 | | | |-- LL_SNVMix_TriTyper |
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| 241 | | | `-- RS_SNVMix_TriTyper |
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| 242 | | `-- RS-imputed-20140306-TriTyper |
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| 243 | |-- rawdata |
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| 244 | | `-- rnaseq |
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| 245 | `-- users |
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| 246 | |-- umcg-aclaringbould |
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| 247 | | |-- abun1 |
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| 248 | | |-- abun2 |
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| 249 | | |-- abun3 |
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| 250 | | |-- bbmri_duplicates |
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| 251 | | |-- eQTLpipeline |
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| 252 | | | |-- backup |
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| 253 | | | |-- cis |
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| 254 | | | |-- first_norm |
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| 255 | | | `-- mixupmapping |
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| 256 | | | |-- Cis-eQTLs |
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| 257 | | | |-- CODAM |
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| 258 | | | | |-- Cis-eQTLs |
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| 259 | | | | `-- MixupMapper |
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| 260 | | | |-- LL |
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| 261 | | | | |-- Cis-eQTLs |
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| 262 | | | | `-- MixupMapper |
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| 263 | | | |-- LLS |
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| 264 | | | | |-- Cis-eQTLs |
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| 265 | | | | `-- MixupMapper |
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| 266 | | | |-- NTR_AC |
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| 267 | | | | |-- Cis-eQTLs |
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| 268 | | | | `-- MixupMapper |
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| 269 | | | |-- NTR_Aff6 |
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| 270 | | | |-- PAN |
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| 271 | | | | |-- Cis-eQTLs |
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| 272 | | | | `-- MixupMapper |
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| 273 | | | `-- RS |
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| 274 | | | |-- Cis-eQTLs |
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| 275 | | | `-- MixupMapper |
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| 276 | | `-- scripts |
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| 277 | `-- umcg-ndeklein |
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| 278 | `-- samplesheets |
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| 279 | |
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| 280 | 277 directories |
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