Module	Section	Sample Name	Source
fastp	all_sections	GSM5772761	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772761.fastp.json
fastp	all_sections	HSCD12_DMSO_1tec	/scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_1tec.fastp.json
fastp	all_sections	HSCD12_DMSO_2tec	/scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_2tec.fastp.json
fastp	all_sections	Skin	/scratch/slrinzema/ghe_2022/metta/qc/trimming/Skin.fastp.json
fastp	all_sections	BoneMarrow	/scratch/slrinzema/ghe_2022/metta/qc/trimming/BoneMarrow.fastp.json
fastp	all_sections	Neutrophil	/scratch/slrinzema/ghe_2022/metta/qc/trimming/Neutrophil.fastp.json
fastp	all_sections	GSM5772762	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772762.fastp.json
fastp	all_sections	CordBlood	/scratch/slrinzema/ghe_2022/metta/qc/trimming/CordBlood.fastp.json
fastp	all_sections	CRISPR	/scratch/slrinzema/ghe_2022/metta/qc/trimming/CRISPR.fastp.json
fastp	all_sections	DMSO_3	/scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_3.fastp.json
fastp	all_sections	GSM6133153	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM6133153.fastp.json
fastp	all_sections	GSM5034742	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5034742.fastp.json
fastp	all_sections	HSCD12_DMSO_3tec	/scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_3tec.fastp.json
fastp	all_sections	GSM6133152	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM6133152.fastp.json
fastp	all_sections	GSM5739838	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739838.fastp.json
fastp	all_sections	DMSO_2	/scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_2.fastp.json
fastp	all_sections	GSM5739833	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739833.fastp.json
fastp	all_sections	GSM5739842	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739842.fastp.json
fastp	all_sections	GSM5772764	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772764.fastp.json
fastp	all_sections	DMSO_1	/scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_1.fastp.json
fastp	all_sections	GSM5772725	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772725.fastp.json
fastp	all_sections	GSM5772763	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772763.fastp.json
fastp	all_sections	GSM5034743	/scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5034743.fastp.json
Picard	InsertSizeMetrics	DMSO_1	/scratch/slrinzema/ghe_2022/metta/qc/InsertSizeMetrics/GRCh38-DMSO_1.tsv
Picard	InsertSizeMetrics	DMSO_2	/scratch/slrinzema/ghe_2022/metta/qc/InsertSizeMetrics/GRCh38-DMSO_2.tsv
Picard	InsertSizeMetrics	CRISPR	/scratch/slrinzema/ghe_2022/metta/qc/InsertSizeMetrics/GRCh38-CRISPR.tsv
Picard	InsertSizeMetrics	CordBlood	/scratch/slrinzema/ghe_2022/metta/qc/InsertSizeMetrics/GRCh38-CordBlood.tsv
Picard	InsertSizeMetrics	DMSO_3	/scratch/slrinzema/ghe_2022/metta/qc/InsertSizeMetrics/GRCh38-DMSO_3.tsv
Picard	DuplicationMetrics	DMSO_3	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-DMSO_3.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	Skin	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-Skin.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	Neutrophil	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-Neutrophil.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	CordBlood	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-CordBlood.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	BoneMarrow	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-BoneMarrow.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	DMSO_2	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-DMSO_2.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	CRISPR	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-CRISPR.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	DMSO_1	/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-DMSO_1.samtools-coordinate.metrics.txt
SamTools pre-sieve	stats	Neutrophil	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-Neutrophil.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	DMSO_2	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-DMSO_2.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	CordBlood	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-CordBlood.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	DMSO_3	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-DMSO_3.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	DMSO_1	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-DMSO_1.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	Skin	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-Skin.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	BoneMarrow	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-BoneMarrow.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	CRISPR	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/star/GRCh38-CRISPR.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	DMSO_3	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-DMSO_3.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	Neutrophil	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-Neutrophil.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	CRISPR	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-CRISPR.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	DMSO_2	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-DMSO_2.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	BoneMarrow	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-BoneMarrow.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	CordBlood	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-CordBlood.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	DMSO_1	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-DMSO_1.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	Skin	/scratch/slrinzema/ghe_2022/metta/qc/samtools_stats/final_bam/GRCh38-Skin.samtools-coordinate.samtools_stats.txt
deepTools	plotPCA	GRCh38	/scratch/slrinzema/ghe_2022/metta/qc/plotPCA/GRCh38.tsv
deepTools	plotFingerprint	GRCh38	/scratch/slrinzema/ghe_2022/metta/qc/plotFingerprint/GRCh38.tsv
Strandedness	infer_experiment	Neutrophil.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-Neutrophil.strandedness.txt
Strandedness	infer_experiment	DMSO_2.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-DMSO_2.strandedness.txt
Strandedness	infer_experiment	CRISPR.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-CRISPR.strandedness.txt
Strandedness	infer_experiment	DMSO_1.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-DMSO_1.strandedness.txt
Strandedness	infer_experiment	BoneMarrow.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-BoneMarrow.strandedness.txt
Strandedness	infer_experiment	DMSO_3.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-DMSO_3.strandedness.txt
Strandedness	infer_experiment	CordBlood.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-CordBlood.strandedness.txt
Strandedness	infer_experiment	Skin.strandedness	/scratch/slrinzema/ghe_2022/metta/qc/strandedness/GRCh38-Skin.strandedness.txt
mtnucratio	all_sections	CordBlood	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-CordBlood.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	DMSO_3	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_3.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	CRISPR	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-CRISPR.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	DMSO_2	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_2.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	Skin	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-Skin.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	Neutrophil	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-Neutrophil.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	BoneMarrow	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-BoneMarrow.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	DMSO_1	/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_1.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json