Module	Section	Sample Name	Source
fastp	all_sections	45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31	/scratch/slrinzema/ghe_2024/results/qc/trimming/45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.fastp.json
fastp	all_sections	45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09	/scratch/slrinzema/ghe_2024/results/qc/trimming/45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.fastp.json
fastp	all_sections	45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27	/scratch/slrinzema/ghe_2024/results/qc/trimming/45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.fastp.json
fastp	all_sections	45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04	/scratch/slrinzema/ghe_2024/results/qc/trimming/45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.fastp.json
Picard	InsertSizeMetrics	45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/TAIR10-45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.tsv
Picard	InsertSizeMetrics	45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/TAIR10-45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.tsv
Picard	InsertSizeMetrics	45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/TAIR10-45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.tsv
Picard	InsertSizeMetrics	45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31	/scratch/slrinzema/ghe_2024/results/qc/InsertSizeMetrics/TAIR10-45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.tsv
Picard	DuplicationMetrics	45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31	/scratch/slrinzema/ghe_2024/results/qc/markdup/TAIR10-45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09	/scratch/slrinzema/ghe_2024/results/qc/markdup/TAIR10-45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04	/scratch/slrinzema/ghe_2024/results/qc/markdup/TAIR10-45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27	/scratch/slrinzema/ghe_2024/results/qc/markdup/TAIR10-45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.samtools-coordinate.metrics.txt
SamTools pre-sieve	stats	45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/TAIR10-45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/TAIR10-45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/TAIR10-45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/star/TAIR10-45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/TAIR10-45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/TAIR10-45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/TAIR10-45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27	/scratch/slrinzema/ghe_2024/results/qc/samtools_stats/final_bam/TAIR10-45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.samtools-coordinate.samtools_stats.txt
deepTools	plotPCA	TAIR10	/scratch/slrinzema/ghe_2024/results/qc/plotPCA/TAIR10.tsv
deepTools	plotFingerprint	TAIR10	/scratch/slrinzema/ghe_2024/results/qc/plotFingerprint/TAIR10.tsv
Strandedness	infer_experiment	45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/TAIR10-45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.strandedness.txt
Strandedness	infer_experiment	45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/TAIR10-45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.strandedness.txt
Strandedness	infer_experiment	45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/TAIR10-45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.strandedness.txt
Strandedness	infer_experiment	45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.strandedness	/scratch/slrinzema/ghe_2024/results/qc/strandedness/TAIR10-45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.strandedness.txt
mtnucratio	all_sections	45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04	/scratch/slrinzema/ghe_2024/results/star/TAIR10-45943_Exp215_GHEtest_7_S1_Arabidopsis__RiboErase_220_A04.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09	/scratch/slrinzema/ghe_2024/results/star/TAIR10-45944_Exp215_GHEtest_8_S2_Arabidopsis_RiboErase_290_A09.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27	/scratch/slrinzema/ghe_2024/results/star/TAIR10-45945_Exp215_GHEtest_11_S1_Arabidopsis_noRibo_A27.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31	/scratch/slrinzema/ghe_2024/results/star/TAIR10-45946_Exp215_GHEtest_12_S2_Arabidopsis_noRibo_A31.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json