Module	Section	Sample Name	Source
QualiMap	genome_results	ACR-178-TP2_S1	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-178-TP2_S1.sorted/genome_results.txt
QualiMap	genome_results	ACR-173-TP2_S4	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-173-TP2_S4.sorted/genome_results.txt
QualiMap	genome_results	ACR-140-TP2_S5	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-140-TP2_S5.sorted/genome_results.txt
QualiMap	genome_results	ACR-150-TP2_S2	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-150-TP2_S2.sorted/genome_results.txt
QualiMap	genome_results	ACR-145-TP2_S3	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-145-TP2_S3.sorted/genome_results.txt
QualiMap	coverage_histogram	ACR-178-TP2_S1	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-178-TP2_S1.sorted/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	ACR-173-TP2_S4	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-173-TP2_S4.sorted/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	ACR-140-TP2_S5	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-140-TP2_S5.sorted/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	ACR-150-TP2_S2	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-150-TP2_S2.sorted/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	ACR-145-TP2_S3	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-145-TP2_S3.sorted/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	insert_size_histogram	ACR-178-TP2_S1	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-178-TP2_S1.sorted/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	ACR-173-TP2_S4	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-173-TP2_S4.sorted/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	ACR-140-TP2_S5	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-140-TP2_S5.sorted/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	ACR-150-TP2_S2	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-150-TP2_S2.sorted/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	ACR-145-TP2_S3	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-145-TP2_S3.sorted/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	mapped_gc_distribution	ACR-178-TP2_S1	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-178-TP2_S1.sorted/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	ACR-173-TP2_S4	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-173-TP2_S4.sorted/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	ACR-140-TP2_S5	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-140-TP2_S5.sorted/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	ACR-150-TP2_S2	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-150-TP2_S2.sorted/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	ACR-145-TP2_S3	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/qualimap/bamqc/ACR-145-TP2_S3.sorted/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
Bismark	alignment	trimmed_ACR-140-TP2_S5_PE_report	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-140-TP2_S5_PE_report.txt
Bismark	alignment	trimmed_ACR-150-TP2_S2_PE_report	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-150-TP2_S2_PE_report.txt
Bismark	alignment	trimmed_ACR-145-TP2_S3_PE_report	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-145-TP2_S3_PE_report.txt
Bismark	alignment	trimmed_ACR-178-TP2_S1_PE_report	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-178-TP2_S1_PE_report.txt
Bismark	alignment	trimmed_ACR-173-TP2_S4_PE_report	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-173-TP2_S4_PE_report.txt
Bismark	deduplication	trimmed_ACR-140-TP2_S5_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-140-TP2_S5_pe.deduplication_report.txt
Bismark	deduplication	trimmed_ACR-173-TP2_S4_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-173-TP2_S4_pe.deduplication_report.txt
Bismark	deduplication	trimmed_ACR-178-TP2_S1_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-178-TP2_S1_pe.deduplication_report.txt
Bismark	deduplication	trimmed_ACR-150-TP2_S2_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-150-TP2_S2_pe.deduplication_report.txt
Bismark	deduplication	trimmed_ACR-145-TP2_S3_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-145-TP2_S3_pe.deduplication_report.txt
Bismark	methylation_extraction	trimmed_ACR-150-TP2_S2_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-150-TP2_S2_pe.deduplicated_splitting_report.txt
Bismark	methylation_extraction	trimmed_ACR-178-TP2_S1_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-178-TP2_S1_pe.deduplicated_splitting_report.txt
Bismark	methylation_extraction	trimmed_ACR-145-TP2_S3_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-145-TP2_S3_pe.deduplicated_splitting_report.txt
Bismark	methylation_extraction	trimmed_ACR-140-TP2_S5_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-140-TP2_S5_pe.deduplicated_splitting_report.txt
Bismark	methylation_extraction	trimmed_ACR-173-TP2_S4_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-173-TP2_S4_pe.deduplicated_splitting_report.txt
Bismark	m_bias	trimmed_ACR-145-TP2_S3_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-145-TP2_S3_pe.deduplicated.M-bias.txt
Bismark	m_bias	trimmed_ACR-173-TP2_S4_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-173-TP2_S4_pe.deduplicated.M-bias.txt
Bismark	m_bias	trimmed_ACR-140-TP2_S5_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-140-TP2_S5_pe.deduplicated.M-bias.txt
Bismark	m_bias	trimmed_ACR-150-TP2_S2_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-150-TP2_S2_pe.deduplicated.M-bias.txt
Bismark	m_bias	trimmed_ACR-178-TP2_S1_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-178-TP2_S1_pe.deduplicated.M-bias.txt
Bismark	bam2nuc	trimmed_ACR-140-TP2_S5_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-140-TP2_S5_pe.deduplicated.nucleotide_stats.txt
Bismark	bam2nuc	trimmed_ACR-145-TP2_S3_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-145-TP2_S3_pe.deduplicated.nucleotide_stats.txt
Bismark	bam2nuc	trimmed_ACR-173-TP2_S4_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-173-TP2_S4_pe.deduplicated.nucleotide_stats.txt
Bismark	bam2nuc	trimmed_ACR-178-TP2_S1_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-178-TP2_S1_pe.deduplicated.nucleotide_stats.txt
Bismark	bam2nuc	trimmed_ACR-150-TP2_S2_pe	/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/trimmed_ACR-150-TP2_S2_pe.deduplicated.nucleotide_stats.txt