Module	Section	Sample Name	Source
MACS2	all_sections	G208M11_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/G208M11_MACS2_output/G208M11_broad_MACS2_peaks.xls
MACS2	all_sections	G208M11_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/G208M11_MACS2_output/G208M11_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M11_TRIM_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/G208M11_TRIM_MACS2_output/G208M11_TRIM_broad_MACS2_peaks.xls
MACS2	all_sections	G208M11_TRIM_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/G208M11_TRIM_MACS2_output/G208M11_TRIM_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M12_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/G208M12_MACS2_output/G208M12_broad_MACS2_peaks.xls
MACS2	all_sections	G208M12_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/G208M12_MACS2_output/G208M12_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M12_TRIM_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/G208M12_TRIM_MACS2_output/G208M12_TRIM_broad_MACS2_peaks.xls
MACS2	all_sections	G208M12_TRIM_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/G208M12_TRIM_MACS2_output/G208M12_TRIM_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M13_TRIM_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/G208M13_TRIM_MACS2_output/G208M13_TRIM_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M13_TRIM_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/G208M13_TRIM_MACS2_output/G208M13_TRIM_broad_MACS2_peaks.xls
MACS2	all_sections	G208M13_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/G208M13_MACS2_output/G208M13_broad_MACS2_peaks.xls
MACS2	all_sections	G208M13_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/G208M13_MACS2_output/G208M13_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M14_TRIM_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/G208M14_TRIM_MACS2_output/G208M14_TRIM_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M14_TRIM_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/G208M14_TRIM_MACS2_output/G208M14_TRIM_broad_MACS2_peaks.xls
MACS2	all_sections	G208M14_narrow_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/G208M14_MACS2_output/G208M14_narrow_MACS2_peaks.xls
MACS2	all_sections	G208M14_broad_MACS2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/G208M14_MACS2_output/G208M14_broad_MACS2_peaks.xls
Picard	InsertSizeMetrics	G208M11_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M11_metrics
Picard	InsertSizeMetrics	G208M11_TRIM_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M11_TRIM_metrics
Picard	InsertSizeMetrics	G208M12_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M12_metrics
Picard	InsertSizeMetrics	G208M12_TRIM_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M12_TRIM_metrics
Picard	InsertSizeMetrics	G208M13_TRIM_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M13_TRIM_metrics
Picard	InsertSizeMetrics	G208M13_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M13_metrics
Picard	InsertSizeMetrics	G208M14_TRIM_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M14_TRIM_metrics
Picard	InsertSizeMetrics	G208M14_sorted_mapped	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/CollectInsertSizeMetrics/G208M14_metrics
Samtools	flagstat	flagstat_G208M11_TRIM	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/flagstat_G208M11_TRIM.txt
Samtools	flagstat	flagstat_G208M12_TRIM	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/flagstat_G208M12_TRIM.txt
Samtools	flagstat	flagstat_G208M13_TRIM	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/flagstat_G208M13_TRIM.txt
Samtools	flagstat	flagstat_G208M14_TRIM	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/flagstat_G208M14_TRIM.txt
Samtools	idxstats	G208M11_TRIM_idxstats	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/bowtie2/G208M11_TRIM_idxstats.out
Samtools	idxstats	G208M12_TRIM_idxstats	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/bowtie2/G208M12_TRIM_idxstats.out
Samtools	idxstats	G208M13_TRIM_idxstats	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/bowtie2/G208M13_TRIM_idxstats.out
Samtools	idxstats	G208M14_TRIM_idxstats	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/bowtie2/G208M14_TRIM_idxstats.out
Bowtie 2 / HiSAT2	all_sections	G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/04_Bowtie2/Step_04_G208_SG_CUTRUN_K27ac_G208M12_TRIM.o76985
Bowtie 2 / HiSAT2	all_sections	G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/04_Bowtie2/Step_04_G208_SG_CUTRUN_K27ac_G208M13_TRIM.o76986
Bowtie 2 / HiSAT2	all_sections	G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/04_Bowtie2/Step_04_G208_SG_CUTRUN_K27ac_G208M11_TRIM.o76984
Bowtie 2 / HiSAT2	all_sections	README_Bowtie2.sh	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/04_Bowtie2/README_Bowtie2.sh
Bowtie 2 / HiSAT2	all_sections	G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/04_Bowtie2/Step_04_G208_SG_CUTRUN_K27ac_G208M14_TRIM.o76987
Cutadapt	all_sections	G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/trim_galore_output/G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M11_TRIM/fastq/trim_galore_output/G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/trim_galore_output/G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M12_TRIM/fastq/trim_galore_output/G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/trim_galore_output/G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M13_TRIM/fastq/trim_galore_output/G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/trim_galore_output/G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/G208M14_TRIM/fastq/trim_galore_output/G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R2.fastq.gz_trimming_report.txt
FastQC	all_sections	G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M13_TRIM_FASTQC/G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R2_fastqc.zip
FastQC	all_sections	G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M13_TRIM_FASTQC/G208M13_CKDL230025721-1A_HGLT2DSX7_L1_R1_fastqc.zip
FastQC	all_sections	G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M11_TRIM_FASTQC/G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R2_fastqc.zip
FastQC	all_sections	G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M11_TRIM_FASTQC/G208M11_CKDL230025721-1A_HGLT2DSX7_L1_R1_fastqc.zip
FastQC	all_sections	G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M12_TRIM_FASTQC/G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R2_fastqc.zip
FastQC	all_sections	G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M12_TRIM_FASTQC/G208M12_CKDL230025721-1A_HGLT2DSX7_L1_R1_fastqc.zip
FastQC	all_sections	G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R2	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M14_TRIM_FASTQC/G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R2_fastqc.zip
FastQC	all_sections	G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R1	/projectnb/wax-dk/max/G208_SG_CUTRUN_K27ac/Scripts/02_FASTQC/Job_Summary/G208M14_TRIM_FASTQC/G208M14_CKDL230025721-1A_HGLT2DSX7_L1_R1_fastqc.zip