Module	Section	Sample Name	Source
Picard	DuplicationMetrics	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/101/DE-1.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/99/DE-2.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/100/DE-3.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/97/DE-3C.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/103/DE-4.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/98/DE-5.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/102/DE-6.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/95/DE-7.markdup.sorted.MarkDuplicates.metrics.txt
Picard	DuplicationMetrics	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/96/HB.markdup.sorted.MarkDuplicates.metrics.txt
QualiMap	rna_genome_results	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/220/DE-1/rnaseq_qc_results.txt
QualiMap	rna_genome_results	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/218/DE-3/rnaseq_qc_results.txt
QualiMap	rna_genome_results	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/215/HB/rnaseq_qc_results.txt
QualiMap	rna_genome_results	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/216/DE-5/rnaseq_qc_results.txt
QualiMap	rna_genome_results	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/214/DE-7/rnaseq_qc_results.txt
QualiMap	rna_genome_results	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/221/DE-6/rnaseq_qc_results.txt
QualiMap	rna_genome_results	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/219/DE-2/rnaseq_qc_results.txt
QualiMap	rna_genome_results	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/217/DE-3C/rnaseq_qc_results.txt
QualiMap	rna_genome_results	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/222/DE-4/rnaseq_qc_results.txt
QualiMap	rna_coverage_histogram	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/220/DE-1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/218/DE-3/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/215/HB/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/216/DE-5/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/214/DE-7/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/221/DE-6/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/219/DE-2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/217/DE-3C/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
QualiMap	rna_coverage_histogram	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/222/DE-4/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt
RSeQC	read_distribution	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/184/DE-1.read_distribution.txt
RSeQC	read_distribution	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/182/DE-2.read_distribution.txt
RSeQC	read_distribution	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/183/DE-3.read_distribution.txt
RSeQC	read_distribution	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/181/DE-3C.read_distribution.txt
RSeQC	read_distribution	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/186/DE-4.read_distribution.txt
RSeQC	read_distribution	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/180/DE-5.read_distribution.txt
RSeQC	read_distribution	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/185/DE-6.read_distribution.txt
RSeQC	read_distribution	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/178/DE-7.read_distribution.txt
RSeQC	read_distribution	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/179/HB.read_distribution.txt
RSeQC	inner_distance	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/128/DE-1.inner_distance_freq.txt
RSeQC	inner_distance	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/126/DE-2.inner_distance_freq.txt
RSeQC	inner_distance	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/127/DE-3.inner_distance_freq.txt
RSeQC	inner_distance	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/124/DE-3C.inner_distance_freq.txt
RSeQC	inner_distance	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/130/DE-4.inner_distance_freq.txt
RSeQC	inner_distance	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/125/DE-5.inner_distance_freq.txt
RSeQC	inner_distance	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/129/DE-6.inner_distance_freq.txt
RSeQC	inner_distance	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/122/DE-7.inner_distance_freq.txt
RSeQC	inner_distance	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/123/HB.inner_distance_freq.txt
RSeQC	read_duplication	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/193/DE-1.pos.DupRate.xls
RSeQC	read_duplication	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/191/DE-2.pos.DupRate.xls
RSeQC	read_duplication	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/192/DE-3.pos.DupRate.xls
RSeQC	read_duplication	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/189/DE-3C.pos.DupRate.xls
RSeQC	read_duplication	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/195/DE-4.pos.DupRate.xls
RSeQC	read_duplication	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/190/DE-5.pos.DupRate.xls
RSeQC	read_duplication	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/194/DE-6.pos.DupRate.xls
RSeQC	read_duplication	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/187/DE-7.pos.DupRate.xls
RSeQC	read_duplication	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/188/HB.pos.DupRate.xls
RSeQC	junction_annotation	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/156/DE-1.junction_annotation.log
RSeQC	junction_annotation	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/154/DE-2.junction_annotation.log
RSeQC	junction_annotation	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/155/DE-3.junction_annotation.log
RSeQC	junction_annotation	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/152/DE-3C.junction_annotation.log
RSeQC	junction_annotation	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/158/DE-4.junction_annotation.log
RSeQC	junction_annotation	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/153/DE-5.junction_annotation.log
RSeQC	junction_annotation	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/157/DE-6.junction_annotation.log
RSeQC	junction_annotation	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/150/DE-7.junction_annotation.log
RSeQC	junction_annotation	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/151/HB.junction_annotation.log
RSeQC	junction_saturation	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/165/DE-1.junctionSaturation_plot.r
RSeQC	junction_saturation	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/163/DE-2.junctionSaturation_plot.r
RSeQC	junction_saturation	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/164/DE-3.junctionSaturation_plot.r
RSeQC	junction_saturation	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/161/DE-3C.junctionSaturation_plot.r
RSeQC	junction_saturation	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/167/DE-4.junctionSaturation_plot.r
RSeQC	junction_saturation	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/162/DE-5.junctionSaturation_plot.r
RSeQC	junction_saturation	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/166/DE-6.junctionSaturation_plot.r
RSeQC	junction_saturation	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/159/DE-7.junctionSaturation_plot.r
RSeQC	junction_saturation	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/160/HB.junctionSaturation_plot.r
RSeQC	infer_experiment	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/137/DE-1.infer_experiment.txt
RSeQC	infer_experiment	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/135/DE-2.infer_experiment.txt
RSeQC	infer_experiment	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/136/DE-3.infer_experiment.txt
RSeQC	infer_experiment	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/134/DE-3C.infer_experiment.txt
RSeQC	infer_experiment	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/139/DE-4.infer_experiment.txt
RSeQC	infer_experiment	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/133/DE-5.infer_experiment.txt
RSeQC	infer_experiment	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/138/DE-6.infer_experiment.txt
RSeQC	infer_experiment	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/131/DE-7.infer_experiment.txt
RSeQC	infer_experiment	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/132/HB.infer_experiment.txt
RSeQC	bam_stat	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/147/DE-1.bam_stat.txt
RSeQC	bam_stat	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/145/DE-2.bam_stat.txt
RSeQC	bam_stat	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/146/DE-3.bam_stat.txt
RSeQC	bam_stat	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/143/DE-3C.bam_stat.txt
RSeQC	bam_stat	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/149/DE-4.bam_stat.txt
RSeQC	bam_stat	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/144/DE-5.bam_stat.txt
RSeQC	bam_stat	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/148/DE-6.bam_stat.txt
RSeQC	bam_stat	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/141/DE-7.bam_stat.txt
RSeQC	bam_stat	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/142/HB.bam_stat.txt
Samtools	stats	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/171/DE-1.markdup.sorted.bam.stats
Samtools	stats	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/92/DE-2.sorted.bam.stats
Samtools	stats	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/174/DE-3.markdup.sorted.bam.stats
Samtools	stats	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/176/DE-3C.markdup.sorted.bam.stats
Samtools	stats	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/88/DE-4.sorted.bam.stats
Samtools	stats	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/84/DE-5.sorted.bam.stats
Samtools	stats	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/169/DE-6.markdup.sorted.bam.stats
Samtools	stats	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/170/DE-7.markdup.sorted.bam.stats
Samtools	stats	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/86/HB.sorted.bam.stats
Samtools	flagstat	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/77/DE-1.sorted.bam.flagstat
Samtools	flagstat	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/121/DE-2.markdup.sorted.bam.flagstat
Samtools	flagstat	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/80/DE-3.sorted.bam.flagstat
Samtools	flagstat	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/82/DE-3C.sorted.bam.flagstat
Samtools	flagstat	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/78/DE-4.sorted.bam.flagstat
Samtools	flagstat	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/115/DE-5.markdup.sorted.bam.flagstat
Samtools	flagstat	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/113/DE-6.markdup.sorted.bam.flagstat
Samtools	flagstat	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/119/DE-7.markdup.sorted.bam.flagstat
Samtools	flagstat	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/114/HB.markdup.sorted.bam.flagstat
Samtools	idxstats	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/104/DE-1.markdup.sorted.bam.idxstats
Samtools	idxstats	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/110/DE-2.markdup.sorted.bam.idxstats
Samtools	idxstats	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/71/DE-3.sorted.bam.idxstats
Samtools	idxstats	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/108/DE-3C.markdup.sorted.bam.idxstats
Samtools	idxstats	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/68/DE-4.sorted.bam.idxstats
Samtools	idxstats	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/69/DE-5.sorted.bam.idxstats
Samtools	idxstats	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/74/DE-6.sorted.bam.idxstats
Samtools	idxstats	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/109/DE-7.markdup.sorted.bam.idxstats
Samtools	idxstats	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/107/HB.markdup.sorted.bam.idxstats
STAR	SummaryLog	DE-1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/63/DE-1.Log.final.out
STAR	SummaryLog	DE-2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/61/DE-2.Log.final.out
STAR	SummaryLog	DE-3	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/62/DE-3.Log.final.out
STAR	SummaryLog	DE-3C	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/60/DE-3C.Log.final.out
STAR	SummaryLog	DE-4	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/65/DE-4.Log.final.out
STAR	SummaryLog	DE-5	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/59/DE-5.Log.final.out
STAR	SummaryLog	DE-6	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/64/DE-6.Log.final.out
STAR	SummaryLog	DE-7	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/57/DE-7.Log.final.out
STAR	SummaryLog	HB	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/58/HB.Log.final.out
FastQC (raw)	all_sections	DE-1_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/15/DE-1_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-1_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/16/DE-1_raw_2_fastqc.zip
FastQC (raw)	all_sections	DE-2_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/13/DE-2_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-2_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/14/DE-2_raw_2_fastqc.zip
FastQC (raw)	all_sections	DE-3C_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/7/DE-3C_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-3C_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/8/DE-3C_raw_2_fastqc.zip
FastQC (raw)	all_sections	DE-3_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/11/DE-3_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-3_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/12/DE-3_raw_2_fastqc.zip
FastQC (raw)	all_sections	DE-4_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/19/DE-4_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-4_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/20/DE-4_raw_2_fastqc.zip
FastQC (raw)	all_sections	DE-5_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/9/DE-5_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-5_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/10/DE-5_raw_2_fastqc.zip
FastQC (raw)	all_sections	DE-6_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/17/DE-6_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-6_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/18/DE-6_raw_2_fastqc.zip
FastQC (raw)	all_sections	DE-7_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/3/DE-7_raw_1_fastqc.zip
FastQC (raw)	all_sections	DE-7_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/4/DE-7_raw_2_fastqc.zip
FastQC (raw)	all_sections	HB_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/5/HB_raw_1_fastqc.zip
FastQC (raw)	all_sections	HB_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/6/HB_raw_2_fastqc.zip
Cutadapt	all_sections	DE-1_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/45/DE-1_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-1_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/46/DE-1_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-2_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/41/DE-2_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-2_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/42/DE-2_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-3C_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/29/DE-3C_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-3C_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/30/DE-3C_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-3_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/37/DE-3_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-3_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/38/DE-3_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-4_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/53/DE-4_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-4_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/54/DE-4_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-5_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/33/DE-5_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-5_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/34/DE-5_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-6_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/49/DE-6_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-6_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/50/DE-6_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-7_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/21/DE-7_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	DE-7_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/22/DE-7_trimmed_2.fastq.gz_trimming_report.txt
Cutadapt	all_sections	HB_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/25/HB_trimmed_1.fastq.gz_trimming_report.txt
Cutadapt	all_sections	HB_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/26/HB_trimmed_2.fastq.gz_trimming_report.txt
FastQC (trimmed)	all_sections	DE-1_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/47/DE-1_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-1_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/48/DE-1_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	DE-2_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/43/DE-2_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-2_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/44/DE-2_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	DE-3C_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/31/DE-3C_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-3C_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/32/DE-3C_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	DE-3_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/39/DE-3_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-3_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/40/DE-3_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	DE-4_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/55/DE-4_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-4_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/56/DE-4_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	DE-5_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/35/DE-5_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-5_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/36/DE-5_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	DE-6_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/51/DE-6_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-6_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/52/DE-6_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	DE-7_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/23/DE-7_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	DE-7_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/24/DE-7_trimmed_2_val_2_fastqc.zip
FastQC (trimmed)	all_sections	HB_1	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/27/HB_trimmed_1_val_1_fastqc.zip
FastQC (trimmed)	all_sections	HB_2	/abyss/gibcus/gibcus_mnt_genomics/basespace/JHG_RNA-seq/work/38/8594575fcebe06521e8b0f18257d47/28/HB_trimmed_2_val_2_fastqc.zip