Module	Section	Sample Name	Source
fastp	all_sections	45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02	/scratch/slrinzema/ghe_2024/results/qc/trimming/45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.fastp.json
fastp	all_sections	45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23	/scratch/slrinzema/ghe_2024/results/qc/trimming/45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.fastp.json
fastp	all_sections	45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21	/scratch/slrinzema/ghe_2024/results/qc/trimming/45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.fastp.json
fastp	all_sections	45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24	/scratch/slrinzema/ghe_2024/results/qc/trimming/45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.fastp.json
fastp	all_sections	45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01	/scratch/slrinzema/ghe_2024/results/qc/trimming/45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.fastp.json
fastp	all_sections	45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22	/scratch/slrinzema/ghe_2024/results/qc/trimming/45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.fastp.json
Picard	InsertSizeMetrics	45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/hg38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.tsv
Picard	InsertSizeMetrics	45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/hg38-45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.tsv
Picard	InsertSizeMetrics	45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/hg38-45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.tsv
Picard	InsertSizeMetrics	45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/hg38-45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.tsv
Picard	InsertSizeMetrics	45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/hg38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.tsv
Picard	InsertSizeMetrics	45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/hg38-45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.tsv
Picard	DuplicationMetrics	45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01	/scratch/slrinzema/ghe_2024/results/qc/markdup/hg38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24	/scratch/slrinzema/ghe_2024/results/qc/markdup/hg38-45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23	/scratch/slrinzema/ghe_2024/results/qc/markdup/hg38-45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21	/scratch/slrinzema/ghe_2024/results/qc/markdup/hg38-45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02	/scratch/slrinzema/ghe_2024/results/qc/markdup/hg38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22	/scratch/slrinzema/ghe_2024/results/qc/markdup/hg38-45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.samtools-coordinate.metrics.txt
SamTools pre-sieve	stats	45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/hg38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/hg38-45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/hg38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/hg38-45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/hg38-45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/hg38-45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/hg38-45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/hg38-45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/hg38-45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/hg38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/hg38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/hg38-45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.samtools-coordinate.samtools_stats.txt
deepTools	plotPCA	hg38	/scratch/slrinzema/ghe_2024/results/qc/plotPCA/hg38.tsv
deepTools	plotFingerprint	hg38	/scratch/slrinzema/ghe_2024/results/qc/plotFingerprint/hg38.tsv
Strandedness	infer_experiment	45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/hg38-45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.strandedness.txt
Strandedness	infer_experiment	45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/hg38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.strandedness.txt
Strandedness	infer_experiment	45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/hg38-45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.strandedness.txt
Strandedness	infer_experiment	45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/hg38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.strandedness.txt
Strandedness	infer_experiment	45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/hg38-45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.strandedness.txt
Strandedness	infer_experiment	45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/hg38-45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.strandedness.txt
mtnucratio	all_sections	45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24	/scratch/slrinzema/ghe_2024/results/star/hg38-45940_Exp215_GHEtest_4_S2_IPSC_noRibo_A24.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21	/scratch/slrinzema/ghe_2024/results/star/hg38-45937_Exp215_GHEtest_1_S1_IPSC_mRNA_A21.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22	/scratch/slrinzema/ghe_2024/results/star/hg38-45938_Exp215_GHEtest_2_S2_IPSC_mRNA_A22.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23	/scratch/slrinzema/ghe_2024/results/star/hg38-45939_Exp215_GHEtest_3_S1_IPSC_noRibo_A23.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02	/scratch/slrinzema/ghe_2024/results/star/hg38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01	/scratch/slrinzema/ghe_2024/results/star/hg38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json