4. Results structure
This folder contains all the fastq quality control (fastQC) reports for each fastq file and a summary report from multiQC.
The fastq reads (R1 and R2) are aligned separately and for each sample two bam files are generated besides the standard out and error files in the contained in the log folder.
If required by the user, in this folder are contained the filtered bams files of the reads used to generate the Hi-C contact matrices. When the bams are not generated because not required, an empty folder named 03_BAM__not_generated is used instead.
This folder contains the "raw" Hi-C contact matrices (.h5 and .cool format) for each sample. Further, in the QC_matrices there are individual folders with the quality controls (QC) performed on each sample and an ALL_SAMPLES folder with all the QC combined in a multiQC-HiC report.
Individual normalized matrices in .h5 format. This matrices are also used to generate correlation heatmaps and scatter plots available in the sample_correlation folder.
In this folder three different subfolder are generated:
- median_absolute_deviation (MAD): calculation of the MAD depending of the coverage per bin (and statistical threshold used for the matrices correction).
- diagnostic_plot: histograms to show the distribution of the coverage per bin used to calculate the MADs.
- corrected_matrices: Hi-C contact normalized and corrected matrices in .h5, .cool and (if required) .hicpro format.
- HiCExplorer: Topologically Associated Domains (TADs) files generated using HiCexplorer: domains and domain's boundaries regions, z-score matrices and TAD scores.
- GENOVA: Topologically Associated Domains (TADs) files generated using GENOVA: domains (.bed), insulation score (.bedGraph) and the insulation discovery object (.RData) importable in R.
Plots of the distribution of the intra-chromosomal contact counts as function of the genomic distance.
If required by the user, the folder contains .bedpe files (chr1 start1 end1 chr2 start2 end2) indicating the anchors/bases of the loops detected in each sample using HiCexplorer or Mustache.
For each resolution, when required, differential compartment analyses are performed using dcHiC. Comparisons are made depending on the groups indicated in the sample config file; samples are compared either all together (all groups) or two-by-two wise by group. Differential compartment analyses are written in the DifferentialResult folder in a folder by comparison. In each comparison subfolder can be found the bedGraphs and bigWigs with the unnormalized and quantile-normalized compartment scores as well as the IGV reports (viz directory). Importantly, in the main parental folder there are the <condition>_chr_pc_selected.txt files that show which principal component (PC) has been used to define the compartments per each chromosome per each sample/group.
For each resolution for each sample, complete......
This folder contains the same analyses performed above but starting from matrices obtained by merging (sum) individual sample "raw" matrices by group (following the sample config table provided by the user).
In this directory can also be found differential chromatin interaction analyses among all group compbinations as performed by SELFISH.
The benchmarks folder contains, for each rule and step (structure: benchamarks > <rule_name> > <rule_name>-<step_id>.tsv), a table containing some performance and resources usage information:
| colname | type (unit) | description |
|---|---|---|
| s | float (seconds) | Running time in seconds |
| hh.mm.ss | string (-) | Running time in hour, minutes, seconds format |
| max_rss | float (MB) | Maximum "Resident Set Size”, this is the non-swapped physical memory a process has used. |
| max_vms | float (MB) | Maximum “Virtual Memory Size”, this is the total amount of virtual memory used by the process |
| max_uss | float (MB) | “Unique Set Size”, this is the memory which is unique to a process and which would be freed if the process was terminated right now. |
| max_pss | float (MB) | “Proportional Set Size”, is the amount of memory shared with other processes, accounted in a way that the amount is divided evenly between the processes that share it (Linux only) |
| io_in | float (MB) | the number of MB read (cumulative). |
| io_out | float (MB) | the number of MB written (cumulative). |
| mean_load | float (-) | CPU usage over time, divided by the total running time (first row) |
| cpu_time | float(-) | CPU time summed for user and system |
For an experiment including 4 samples (sampleA-B-C-D) assigned to two groups (Normal and Tumor) and for which 2 resolutions will be analyzed (50kb and 100kb), the structure of the output_folder will be the following (... means repetition of the same file pattern as the parental file/folder):
output_folder
├── 01_fastQC_raw
│ ├── multiQC_raw
│ │ ├── multiQC_report_fastqRaw_data
│ │ │ ├── multiqc_citations.txt
│ │ │ ├── multiqc_data.json
│ │ │ ├── multiqc_fastqc.txt
│ │ │ ├── multiqc_general_stats.txt
│ │ │ ├── multiqc.log
│ │ │ └── multiqc_sources.txt
│ │ └── multiQC_report_fastqRaw.html
│ ├── sampleA_R1_fastqc.html
│ ├── sampleA_R1_fastqc.zip
│ ├── sampleA_R2_fastqc.html
│ ├── sampleA_R2_fastqc.zip
│ └── ...
│
├── 02_Alignements
│ ├── log
│ │ ├── sampleA_R1_bwa-mem.err
│ │ ├── sampleA_R1_bwa-mem.out
│ │ ├── sampleA_R2_bwa-mem.err
│ │ ├── sampleA_R2_bwa-mem.out
│ │ └── ...
│ ├── sampleA_R1.bam
│ ├── sampleA_R2.bam
│ └── ...
│
├── 03_BAM / 03_BAM__not_generated
│ ├── falgstat
│ │ ├── sampleA_flagstat_bam.txt
│ │ ├── sampleB_flagstat_bam.txt
│ │ └── ...
│ ├── sampleA_mapQ15_sorted.bam
│ ├── sampleA_mapQ15_sorted.bai
│ └── ...
│
├── 04_Interaction_matrices
│ ├── log
│ │ ├── sampleA.100kb.hicBuildMatrix.err
│ │ ├── sampleA.100kb.hicBuildMatrix.log
│ │ ├── sampleA.50kb.hicBuildMatrix.err
│ │ ├── sampleA.50kb.hicBuildMatrix.log
│ │ └── ...
│ ├── QC_matrices
│ │ ├── ALL_SAMPLES
│ │ │ ├── HiQC_matrices
│ │ │ │ ├── discarded_table.txt
│ │ │ │ ├── distance.png
│ │ │ │ ├── distance_table.txt
│ │ │ │ ├── hicQC.html
│ │ │ │ ├── pairs_discarded.png
│ │ │ │ ├── pairs_sequenced.png
│ │ │ │ ├── QC_table.txt
│ │ │ │ ├── read_orientation.png
│ │ │ │ ├── read_orientation_table.txt
│ │ │ │ ├── unmapable_table.txt
│ │ │ │ └── unmappable_and_non_unique.png
│ │ │ └── multiQC_matrices
│ │ │ ├── multiqc_data
│ │ │ │ ├── multiqc_citations.txt
│ │ │ │ ├── multiqc_data.json
│ │ │ │ ├── multiqc_general_stats.txt
│ │ │ │ ├── multiqc_hicexplorer.txt
│ │ │ │ ├── multiqc.log
│ │ │ │ └── multiqc_sources.txt
│ │ │ └── multiqc_report.html
│ │ ├── sampleA
│ │ │ ├── discarded_table.txt
│ │ │ ├── distance.png
│ │ │ ├── distance_table.txt
│ │ │ ├── hicQC.html
│ │ │ ├── pairs_discarded.png
│ │ │ ├── pairs_sequenced.png
│ │ │ ├── QC.log
│ │ │ ├── QC_table.txt
│ │ │ ├── read_orientation.png
│ │ │ ├── read_orientation_table.txt
│ │ │ ├── unmapable_table.txt
│ │ │ └── unmappable_and_non_unique.png
│ │ └── sample...
│ │ └── ...
│ ├── sampleA_mapQ15_100kb.h5
│ ├── sampleA_mapQ15_50kb.cool
│ ├── sampleA_mapQ15_50kb.h5
│ └── ...
│
├── 05_Interaction_matrices_Normalized
│ ├── sampleA_mapQ15_100kb_Normalized.h5
│ ├── sampleA_mapQ15_50kb_Normalized.h5
│ ├── ...
│ └── sample_correlation
│ ├── heatmap_correlation.pdf
│ └── scatter_correlation.pdf
│
├── 06_Interaction_matrices_Normalized_and_corrected
│ ├── corrected_matrices
│ │ ├── sampleA
│ │ │ ├── cool_format
│ │ │ │ ├── sampleA_mapQ15_100kb_Normalized_corrected.cool
│ │ │ │ └── sampleA_mapQ15_50kb_Normalized_corrected.cool
│ │ │ ├── h5_format
│ │ │ │ ├── sampleA_mapQ15_100kb_Normalized_corrected.h5
│ │ │ │ └── sampleA_mapQ15_50kb_Normalized_corrected.h5
│ │ │ └── hicpro_format
│ │ │ ├── sampleA_mapQ15_100kb_Normalized_corrected.hicpro
│ │ │ ├── sampleA_mapQ15_100kb_Normalized_corrected_hicpro.bed
│ │ │ ├── sampleA_mapQ15_50kb_Normalized_corrected.hicpro
│ │ │ └── sampleA_mapQ15_50kb_Normalized_corrected_hicpro.bed
│ │ └── sample...
│ │ └── ...
│ ├── diagnostic_plots
│ │ ├── sampleA_100kb_Normalized_diagnosticPlot.png
│ │ ├── sampleA_50kb_Normalized_diagnosticPlot.png
│ │ └── ...
│ └── median_absolute_deviation
│ ├── sampleA_100kb_Normalized_MedianAbsoluteDeviation.mad
│ ├── sampleA_50kb_Normalized_MedianAbsoluteDeviation.mad
│ ├── ...
│ └── thresholds
│ ├── sampleA_100kb_Normalized_thresholdValues.txt
│ ├── sampleA_50kb_Normalized_thresholdValues.txt
│ └── ...
│
├── 07_TADs_calling_HiCexplorer
│ ├── sampleA
│ │ ├── 100kb_resolution
│ │ │ ├── log
│ │ │ │ ├── sampleA_mapQ15_100kb_TAD.calling.err
│ │ │ │ └── sampleA_mapQ15_100kb_TAD.calling.out
│ │ │ ├── sampleA_mapQ15_100kb_boundaries.bed
│ │ │ ├── sampleA_mapQ15_100kb_boundaries.gff
│ │ │ ├── sampleA_mapQ15_100kb_domains.bed
│ │ │ ├── sampleA_mapQ15_100kb_score.bedgraph
│ │ │ ├── sampleA_mapQ15_100kb_tad_score.bm
│ │ │ └── sampleA_mapQ15_100kb_zscore_matrix.h5
│ │ └── 50kb_resolution
│ │ ├── log
│ │ │ ├── sampleA_mapQ15_50kb_TAD.calling.err
│ │ │ └── sampleA_mapQ15_50kb_TAD.calling.out
│ │ ├── sampleA_mapQ15_50kb_boundaries.bed
│ │ ├── sampleA_mapQ15_50kb_boundaries.gff
│ │ ├── sampleA_mapQ15_50kb_domains.bed
│ │ ├── sampleA_mapQ15_50kb_score.bedgraph
│ │ ├── sampleA_mapQ15_50kb_tad_score.bm
│ │ └── sampleA_mapQ15_50kb_zscore_matrix.h5
│ └── sample...
│ └── ...
│
├── 08_Interaction_distances
│ ├── intraChr_distances_all_samples_100kb_resolution_distancesValues.tsv
│ ├── intraChr_distances_all_samples_100kb_resolution.pdf
│ ├── intraChr_distances_all_samples_50kb_resolution_distancesValues.tsv
│ ├── intraChr_distances_all_samples_50kb_resolution.pdf
│ └── log
│ ├── intraChr_distances_all_samples_100kb_resolution.err
│ ├── intraChr_distances_all_samples_100kb_resolution.out
│ ├── intraChr_distances_all_samples_50kb_resolution.err
│ └── intraChr_distances_all_samples_50kb_resolution.out
│
├── 09_Loop_detection_HiCexplorer
│ ├── sampleA
│ │ ├── log
│ │ │ ├── sampleA_mapQ15_100kb_loop.detectiong.err
│ │ │ ├── sampleA_mapQ15_100kb_loop.detection.out
│ │ │ ├── sampleA_mapQ15_50kb_loop.detectiong.err
│ │ │ └── sampleA_mapQ15_50kb_loop.detection.out
│ │ ├── sampleA_mapQ15_100kb_loops.bedpe
│ │ └── sampleA_mapQ15_50kb_loops.bedpe
│ └── sample...
│ └── ...
│
├── 10_Compartments_detection_dcHiC
│ ├── 100kb_resolution
│ │ ├── dcHiC_input_file_individual_samples_100kb.txt
│ │ ├── DifferentialResult
│ │ │ └── all_vs_all
│ │ │ ├── Normal_data
│ │ │ ├── pcOri
│ │ │ ├── pcQnm
│ │ │ ├── Tumor_data
│ │ │ └── viz
│ │ │ └── files
│ │ ├── filtered_hicpro_beds
│ │ │ ├── sampleA_mapQ15_100kb_Normalized_corrected_hicpro_FILTERED.bed
│ │ │ └── ...
│ │ ├── hg19_1000000_goldenpathData
│ │ │ ├── cytoBand.txt.gz
│ │ │ ├── hg19.binned.bed
│ │ │ ├── hg19.chrom.sizes
│ │ │ ├── hg19.fa
│ │ │ ├── hg19.fa.fai
│ │ │ ├── hg19.fa.gz
│ │ │ ├── hg19.GCpt.bedGraph
│ │ │ ├── hg19.GCpt.tss.bedGraph
│ │ │ ├── hg19.refGene.gtf.gz
│ │ │ └── hg19.tss.bed
│ │ ├── sampleA_mapQ15_100kb_pca
│ │ │ └── intra_pca
│ │ │ └── sampleA_mapQ15_100kb_mat
│ │ │ ├── chr1.bed
│ │ │ ├── chr1.cmat.txt
│ │ │ ├── chr1.distparam
│ │ │ ├── chr1.pc.txt
│ │ │ ├── chr1.precmat.txt
│ │ │ ├── chr1.svd.rds
│ │ │ ├── chr1.txt
│ │ │ └── ...
│ │ └── sample..._mapQ15_100kb_pca
│ │ └── ...
│ └── 50kb_resolution
│ ├── dcHiC_input_file_individual_samples_50kb_Normal_vs_Tumor.txt
│ ├── dcHiC_input_file_individual_samples_50kb.txt
│ ├── DifferentialResult
│ │ ├── all_vs_all
│ │ │ ├── fdr_result
│ │ │ │ ├── differential.intra_sample_chr1_combined.pcQnm.bedGraph
│ │ │ │ ├── ...
│ │ │ │ ├── differential.intra_sample_combined.Filtered.pcQnm.bedGraph
│ │ │ │ ├── differential.intra_sample_combined.pcQnm.bedGraph
│ │ │ │ ├── differential.intra_sample_group.Filtered.pcOri.bedGraph
│ │ │ │ ├── differential.intra_sample_group.Filtered.pcQnm.bedGraph
│ │ │ │ ├── differential.intra_sample_group.pcOri.bedGraph
│ │ │ │ └── differential.intra_sample_group.pcQnm.bedGraph
│ │ │ ├── Normal_data
│ │ │ │ ├── intra_chr1_combined.pcOri.bedGraph
│ │ │ │ ├── intra_chr1_combined.pcQnm.bedGraph
│ │ │ │ ├── ...
│ │ │ │ ├── sampleB_mapQ15_50kb_intra_chr1.pc.bedGraph
│ │ │ │ ├── ...
│ │ │ │ ├── sampleC_mapQ15_50kb_intra_chr12.pc.bedGraph
│ │ │ │ └── ...
│ │ │ ├── pcOri
│ │ │ │ ├── intra_sample_chr1_combined.pcOri.bedGraph
│ │ │ │ └── ...
│ │ │ ├── pcQnm
│ │ │ │ ├── intra_sample_chr1_combined.pcQnm.bedGraph
│ │ │ │ └── ...
│ │ │ ├── Tumor_data
│ │ │ │ ├── intra_chr1_combined.pcOri.bedGraph
│ │ │ │ └── ...
│ │ │ │ ├── sampleA_mapQ15_50kb_intra_chr1.pc.bedGraph
│ │ │ │ ├── sample..._mapQ15_50kb_intra_chr....pc.bedGraph
│ │ │ │ └── ...
│ │ │ └── viz
│ │ │ ├── files
│ │ │ │ ├── intra_compartment.bedGraph
│ │ │ │ ├── intra_sampleA_mapQ15_50kb_PC_A.compartment.bedGraph
│ │ │ │ ├── intra_sampleA_mapQ15_50kb_PC_B.compartment.bedGraph
│ │ │ │ ├── intra_sampleA_mapQ15_50kb_PC.bedGraph
│ │ │ │ └── ...
│ │ │ ├── files_bigWig
│ │ │ │ ├── intra_sampleA_mapQ15_50kb_PC.bw
│ │ │ │ ├── intra_sampleB_mapQ15_50kb_PC.bw
│ │ │ │ ├── intra_sampleC_mapQ15_50kb_PC.bw
│ │ │ │ └── intra_sampleD_mapQ15_50kb_PC.bw
│ │ │ ├── files_compartment_beds
│ │ │ │ ├── intra_sampleA_mapQ15_50kb_PC_compartments_sorted.bed
│ │ │ │ ├── intra_sampleB_mapQ15_50kb_PC_compartments_sorted.bed
│ │ │ │ ├── intra_sampleC_mapQ15_50kb_PC_compartments_sorted.bed
│ │ │ │ └── intra_sampleD_mapQ15_50kb_PC_compartments_sorted.bed
│ │ │ └── vizIGV_intra
│ │ │ ├── data
│ │ │ │ ├── differential_compartment.log10Padj.bedGraph.gz
│ │ │ │ ├── differential_compartment.Mahalanobis.bedGraph
│ │ │ │ ├── differential_compartment.Mahalanobis.bedGraph.gz
│ │ │ │ ├── Normal.PC.bedGraph.gz
│ │ │ │ └── Tumor.PC.bedGraph.gz
│ │ │ ├── data_bigWig
│ │ │ │ ├── differential_compartment.log10Padj.bw
│ │ │ │ ├── differential_compartment.Mahalanobis.bw
│ │ │ │ ├── Normal.PC.bw
│ │ │ │ └── Tumor.PC.bw
│ │ │ ├── data_compartment_beds
│ │ │ │ ├── Normal.PC_compartments_sorted.bed
│ │ │ │ └── Tumor.PC_compartments_sorted.bed
│ │ │ └── intra_igv_pcQnm.html
│ │ └── Normal_vs_Tumor
│ │ ├── fdr_result
│ │ │ ├── differential.intra_sample_chr1_combined.pcQnm.bedGraph
│ │ │ └── ...
│ │ │ ├── differential.intra_sample_combined.Filtered.pcQnm.bedGraph
│ │ │ ├── differential.intra_sample_combined.pcQnm.bedGraph
│ │ │ ├── differential.intra_sample_group.Filtered.pcOri.bedGraph
│ │ │ ├── differential.intra_sample_group.Filtered.pcQnm.bedGraph
│ │ │ ├── differential.intra_sample_group.pcOri.bedGraph
│ │ │ └── differential.intra_sample_group.pcQnm.bedGraph
│ │ ├── Normal_data
│ │ │ ├── intra_chr1_combined.pcOri.bedGraph
│ │ │ ├── intra_chr1_combined.pcQnm.bedGraph
│ │ │ └── ...
│ │ │ ├── sample..._mapQ15_50kb_intra_chr...pc.bedGraph
│ │ │ └── ...
│ │ ├── pcOri
│ │ │ ├── intra_sample_chr1_combined.pcOri.bedGraph
│ │ │ └── ...
│ │ ├── pcQnm
│ │ │ ├── intra_sample_chr1_combined.pcQnm.bedGraph
│ │ │ └── ...
│ │ ├── Tumor_data
│ │ │ ├── intra_chr1_combined.pcOri.bedGraph
│ │ │ ├── intra_chr1_combined.pcQnm.bedGraph
│ │ │ └── ...
│ │ │ ├── sampleA_mapQ15_50kb_intra_chr1.pc.bedGraph
│ │ │ ├── sample..._mapQ15_50kb_intra_chr....pc.bedGraph
│ │ │ └── ...
│ │ └── viz
│ │ ├── files
│ │ │ ├── intra_compartment.bedGraph
│ │ │ ├── intra_sampleA_mapQ15_50kb_PC_A.compartment.bedGraph
│ │ │ ├── intra_sampleA_mapQ15_50kb_PC_B.compartment.bedGraph
│ │ │ ├── intra_sampleA_mapQ15_50kb_PC.bedGraph
│ │ │ └── ...
│ │ ├── files_bigWig
│ │ │ ├── intra_sampleA_mapQ15_50kb_PC.bw
│ │ │ └── ...
│ │ ├── files_compartment_beds
│ │ │ ├── intra_sampleA_mapQ15_50kb_PC_compartments_sorted.bed
│ │ │ └── ...
│ │ └── vizIGV_intra
│ │ ├── data
│ │ │ ├── differential_compartment.log10Padj.bedGraph.gz
│ │ │ ├── differential_compartment.Mahalanobis.bedGraph
│ │ │ ├── differential_compartment.Mahalanobis.bedGraph.gz
│ │ │ ├── Normal.PC.bedGraph.gz
│ │ │ └── Tumor.PC.bedGraph.gz
│ │ ├── data_bigWig
│ │ │ ├── differential_compartment.log10Padj.bw
│ │ │ ├── differential_compartment.Mahalanobis.bw
│ │ │ ├── Normal.PC.bw
│ │ │ └── Tumor.PC.bw
│ │ ├── data_compartment_beds
│ │ │ ├── Normal.PC_compartments_sorted.bed
│ │ │ └── Tumor.PC_compartments_sorted.bed
│ │ └── intra_igv_pcQnm.html
│ ├── filtered_hicpro_beds
│ │ ├── sampleA_mapQ15_50kb_Normalized_corrected_hicpro_FILTERED.bed
│ │ └── ...
│ ├── hg19_500000_goldenpathData
│ │ ├── cytoBand.txt.gz
│ │ ├── hg19.binned.bed
│ │ ├── hg19.chrom.sizes
│ │ ├── hg19.fa
│ │ ├── hg19.fa.fai
│ │ ├── hg19.fa.gz
│ │ ├── hg19.GCpt.bedGraph
│ │ ├── hg19.GCpt.tss.bedGraph
│ │ ├── hg19.refGene.gtf.gz
│ │ └── hg19.tss.bed
│ ├── Normal_chr_pc_selected.txt
│ ├── Normal_clus.txt
│ ├── Normal_cor.txt
│ ├── Normal_vals.txt
│ ├── sampleA_mapQ15_50kb_pca
│ │ └── intra_pca
│ │ └── sampleA_mapQ15_50kb_mat
│ │ ├── chr1.bed
│ │ ├── chr1.cmat.txt
│ │ ├── chr1.distparam
│ │ ├── chr1.PC1.bedGraph
│ │ ├── chr1.PC2.bedGraph
│ │ ├── chr1.pc.bedGraph
│ │ ├── chr1.pc.txt
│ │ ├── chr1.precmat.txt
│ │ ├── chr1.svd.rds
│ │ ├── chr1.txt
│ │ └── ...
│ ├── sample...
│ │ └── ...
│ ├── Tumor_chr_pc_selected.txt
│ ├── Tumor_clus.txt
│ ├── Tumor_cor.txt
│ └── Tumor_vals.txt
│
├── 11_Stripes_analyses_STREPENN
| ├── sampleA
| │ ├── logs
| | ├── Normal
| | | ├── Normal_50kb
| | | | ├── result_filtered.tsvstripenn.log
| | | | ├── result_unfiltered.tsv
| | | | └── stripenn.log
| | | └── Normal_100kb
| | | └── ...
| | └── ...
| └── ...
|
│ ***************************************************************************************
│
└── 12_Grouped_analyses
├── A_summed_matrices
│ ├── log
│ │ ├── Normal.100kb.hicBuildMatrix.err
│ │ ├── Normal.100kb.hicBuildMatrix.log
│ │ ├── Tumor.100kb.hicBuildMatrix.err
│ │ └── Tumor.100kb.hicBuildMatrix.log
│ ├── Normal_mapQ15_100kb.h5
│ ├── Normal_mapQ15_50kb.h5
│ ├── Tumor_mapQ15_100kb.h5
│ └── Tumor_mapQ15_50kb.h5
|
├── B_summed_matrices_Normalized
│ ├── Normal_mapQ15_100kb_Normalized.h5
│ ├── Normal_mapQ15_50kb_Normalized.h5
│ ├── Tumor_mapQ15_100kb_Normalized.h5
│ └── Tumor_mapQ15_50kb_Normalized.h5
|
├── C_summed_matrices_Normalized_and_corrected
│ ├── corrected_matrices
│ │ ├── Normal
│ │ │ ├── cool_format
│ │ │ │ ├── Normal_mapQ15_100kb_Normalized_corrected.cool
│ │ │ │ └── Normal_mapQ15_50kb_Normalized_corrected.cool
│ │ │ ├── h5_format
│ │ │ │ ├── Normal_mapQ15_100kb_Normalized_corrected.h5
│ │ │ │ └── Normal_mapQ15_50kb_Normalized_corrected.h5
│ │ │ └── hicpro_format
│ │ │ ├── Normal_mapQ15_100kb_Normalized_corrected.hicpro
│ │ │ ├── Normal_mapQ15_100kb_Normalized_corrected_hicpro.bed
│ │ │ ├── Normal_mapQ15_50kb_Normalized_corrected.hicpro
│ │ │ └── Normal_mapQ15_50kb_Normalized_corrected_hicpro.bed
│ │ └── Tumor
│ │ ├── cool_format
│ │ │ ├── Tumor_mapQ15_100kb_Normalized_corrected.cool
│ │ │ └── Tumor_mapQ15_50kb_Normalized_corrected.cool
│ │ ├── h5_format
│ │ │ ├── Tumor_mapQ15_100kb_Normalized_corrected.h5
│ │ │ └── Tumor_mapQ15_50kb_Normalized_corrected.h5
│ │ └── hicpro_format
│ │ ├── Tumor_mapQ15_100kb_Normalized_corrected.hicpro
│ │ ├── Tumor_mapQ15_100kb_Normalized_corrected_hicpro.bed
│ │ ├── Tumor_mapQ15_50kb_Normalized_corrected.hicpro
│ │ └── Tumor_mapQ15_50kb_Normalized_corrected_hicpro.bed
│ ├── diagnostic_plots
│ │ ├── Normal_100kb_Normalized_diagnosticPlot.png
│ │ ├── Normal_50kb_Normalized_diagnosticPlot.png
│ │ ├── Tumor_100kb_Normalized_diagnosticPlot.png
│ │ └── Tumor_50kb_Normalized_diagnosticPlot.png
│ └── median_absolute_deviation
│ ├── Normal_100kb_Normalized_MedianAbsoluteDeviation.mad
│ ├── Normal_50kb_Normalized_MedianAbsoluteDeviation.mad
│ ├── thresholds
│ │ ├── Normal_100kb_Normalized_thresholdValues.txt
│ │ ├── Normal_50kb_Normalized_thresholdValues.txt
│ │ ├── Tumor_100kb_Normalized_thresholdValues.txt
│ │ └── Tumor_50kb_Normalized_thresholdValues.txt
│ ├── Tumor_100kb_Normalized_MedianAbsoluteDeviation.mad
│ └── Tumor_50kb_Normalized_MedianAbsoluteDeviation.mad
|
├── D_TADs_calling_HiCexplorer
│ ├── Normal
│ │ ├── 50kb_resolution
│ │ │ ├── log
│ │ │ | ├── Normal_mapQ15_50kb_TAD.calling.err
│ │ │ | └── Normal_mapQ15_50kb_TAD.calling.out
│ │ │ ├── Normal_mapQ15_50kb_boundaries.bed
│ │ │ ├── Normal_mapQ15_50kb_boundaries.gff
│ │ │ ├── Normal_mapQ15_50kb_domains.bed
│ │ │ ├── Normal_mapQ15_50kb_score.bedgraph
│ │ │ ├── Normal_mapQ15_50kb_tad_score.bm
│ │ │ └── Normal_mapQ15_50kb_zscore_matrix.h5
│ │ └── 100kb_resolution
│ │ └── ...
│ └── Tumor
│ └── ...
├── E_Loop_detection_HiCexplorer
│ ├── Normal
│ │ ├── log
│ │ │ ├── Normal_mapQ15_100kb_loop.detection.err
│ │ │ ├── Normal_mapQ15_100kb_loop.detection.out
│ │ │ ├── Normal_mapQ15_50kb_loop.detection.err
│ │ │ └── Normal_mapQ15_50kb_loop.detection.out
│ │ ├── Normal_mapQ15_100kb_loops.bedpe
│ │ └── Normal_mapQ15_50kb_loops.bedpe
│ └── Tumor
│ └── ...
|
├── F_Compartments_detection_dcHiC
| ├── 50kb_resolution
| │ ├── dcHiC_input_file_grouped_samples_50kb.txt
| │ ├── dcHiC_input_file_individual_samples_50kb_Normal_vs_Tumor.txt
| │ ├── DifferentialResult
| │ | ├── all_vs_all
| │ | │ ├── fdr_result
| │ | │ │ ├── differential.intra_sample_chr1_combined.pcQnm.bedGraph
| │ | │ │ ├── ...
| │ | │ │ ├── differential.intra_sample_combined.Filtered.pcQnm.bedGraph
| │ | │ │ ├── differential.intra_sample_combined.pcQnm.bedGraph
| │ | │ │ ├── differential.intra_sample_group.Filtered.pcOri.bedGraph
| │ | │ │ ├── differential.intra_sample_group.Filtered.pcQnm.bedGraph
| │ | │ │ ├── differential.intra_sample_group.pcOri.bedGraph
| │ | │ │ └── differential.intra_sample_group.pcQnm.bedGraph
| │ | │ ├── Normal_data
| │ | │ │ ├── intra_chr1_combined.pcOri.bedGraph
| │ | │ │ ├── intra_chr1_combined.pcQnm.bedGraph
| │ | │ │ └── ...
| │ | │ │ ├── Normal_mapQ15_50kb_intra_chr1.pc.bedGraph
| │ | │ │ └── ...
| │ | │ ├── pcOri
| │ | │ │ ├── intra_sample_chr1_combined.pcOri.bedGraph
| │ | │ │ └── ...
| │ | │ ├── pcQnm
| │ | │ │ ├── intra_sample_chr1_combined.pcQnm.bedGraph
| │ | │ │ └── ...
| │ | │ ├── Tumor_data
| │ | │ │ ├── intra_chr1_combined.pcOri.bedGraph
| │ | │ │ └── ...
| │ | │ │ ├── Tumor_mapQ15_50kb_intra_chr11.pc.bedGraph
| │ | │ │ └── ...
| │ | │ └── viz
| │ | │ ├── files
| │ | │ │ ├── intra_compartment.bedGraph
| │ | │ │ ├── intra_Normal_mapQ15_50kb_PC_A.compartment.bedGraph
| │ | │ │ ├── intra_Normal_mapQ15_50kb_PC_B.compartment.bedGraph
| │ | │ │ ├── intra_Normal_mapQ15_50kb_PC.bedGraph
| │ | │ │ ├── intra_Tumor_mapQ15_50kb_PC_A.compartment.bedGraph
| │ | │ │ ├── intra_Tumor_mapQ15_50kb_PC_B.compartment.bedGraph
| │ | │ │ └── intra_Tumor_mapQ15_50kb_PC.bedGraph
| │ | │ ├── files_bigWig
| │ | │ │ ├── intra_Normal_mapQ15_50kb_PC.bw
| │ | │ │ └── intra_Tumor_mapQ15_50kb_PC.bw
| │ | │ ├── files_compartment_beds
| │ | │ │ ├── intra_Normal_mapQ15_50kb_PC_compartments_sorted.bed
| │ | │ │ └── intra_Tumor_mapQ15_50kb_PC_compartments_sorted.bed
| │ | │ └── vizIGV_intra
| │ | │ ├── data
| │ | │ │ ├── differential_compartment.log10Padj.bedGraph.gz
| │ | │ │ ├── differential_compartment.Mahalanobis.bedGraph
| │ | │ │ ├── differential_compartment.Mahalanobis.bedGraph.gz
| │ | │ │ ├── Normal.PC.bedGraph.gz
| │ | │ │ └── Tumor.PC.bedGraph.gz
| │ | │ ├── data_bigWig
| │ | │ │ ├── differential_compartment.log10Padj.bw
| │ | │ │ ├── differential_compartment.Mahalanobis.bw
| │ | │ │ ├── Normal.PC.bw
| │ | │ │ └── Tumor.PC.bw
| │ | │ ├── data_compartment_beds
| │ | │ │ ├── Normal.PC_compartments_sorted.bed
| │ | │ │ └── Tumor.PC_compartments_sorted.bed
| │ | │ └── intra_igv_pcQnm.html
| │ | └── Normal_vs_Tumor
| │ | ├── fdr_result
| │ | │ ├── differential.intra_sample_chr1_combined.pcQnm.bedGraph
| │ | │ ├── ...
| │ | │ ├── differential.intra_sample_combined.Filtered.pcQnm.bedGraph
| │ | │ ├── differential.intra_sample_combined.pcQnm.bedGraph
| │ | │ ├── differential.intra_sample_group.Filtered.pcOri.bedGraph
| │ | │ ├── differential.intra_sample_group.Filtered.pcQnm.bedGraph
| │ | │ ├── differential.intra_sample_group.pcOri.bedGraph
| │ | │ └── differential.intra_sample_group.pcQnm.bedGraph
| │ | ├── Normal_data
| │ | │ ├── intra_chr1_combined.pcOri.bedGraph
| │ | │ ├── intra_chr1_combined.pcQnm.bedGraph
| │ | │ └── ...
| │ | │ ├── Normal_mapQ15_50kb_intra_chr1.pc.bedGraph
| │ | │ └── ...
| │ | ├── pcOri
| │ | │ ├── intra_sample_chr1_combined.pcOri.bedGraph
| │ | │ └── ...
| │ | ├── pcQnm
| │ | │ ├── intra_sample_chr1_combined.pcQnm.bedGraph
| │ | │ └── ...
| │ | ├── Tumor_data
| │ | │ ├── intra_chr1_combined.pcOri.bedGraph
| │ | │ └── ...
| │ | └── viz
| │ | ├── files
| │ | │ ├── intra_compartment.bedGraph
| │ | │ ├── intra_Normal_mapQ15_50kb_PC_A.compartment.bedGraph
| │ | │ ├── intra_Normal_mapQ15_50kb_PC_B.compartment.bedGraph
| │ | │ ├── intra_Normal_mapQ15_50kb_PC.bedGraph
| │ | │ ├── intra_Tumor_mapQ15_50kb_PC_A.compartment.bedGraph
| │ | │ ├── intra_Tumor_mapQ15_50kb_PC_B.compartment.bedGraph
| │ | │ └── intra_Tumor_mapQ15_50kb_PC.bedGraph
| │ | ├── files_bigWig
| │ | │ ├── intra_Normal_mapQ15_50kb_PC.bw
| │ | │ └── intra_Tumor_mapQ15_50kb_PC.bw
| │ | ├── files_compartment_beds
| │ | │ ├── intra_Normal_mapQ15_50kb_PC_compartments_sorted.bed
| │ | │ └── intra_Tumor_mapQ15_50kb_PC_compartments_sorted.bed
| │ | └── vizIGV_intra
| │ | ├── data
| │ | │ ├── differential_compartment.log10Padj.bedGraph.gz
| │ | │ ├── differential_compartment.Mahalanobis.bedGraph
| │ | │ ├── differential_compartment.Mahalanobis.bedGraph.gz
| │ | │ ├── Normal.PC.bedGraph.gz
| │ | │ └── Tumor.PC.bedGraph.gz
| │ | ├── data_bigWig
| │ | │ ├── differential_compartment.log10Padj.bw
| │ | │ ├── differential_compartment.Mahalanobis.bw
| │ | │ ├── Normal.PC.bw
| │ | │ └── Tumor.PC.bw
| │ | ├── data_compartment_beds
| │ | │ ├── Normal.PC_compartments_sorted.bed
| │ | │ └── Tumor.PC_compartments_sorted.bed
| │ | └── intra_igv_pcQnm.html
| │ ├── filtered_hicpro_beds
| │ | ├── Normal_mapQ15_50kb_Normalized_corrected_hicpro_FILTERED.bed
| │ | └── Tumor_mapQ15_50kb_Normalized_corrected_hicpro_FILTERED.bed
| │ ├── hg19_500000_goldenpathData
| │ | ├── cytoBand.txt.gz
| │ | ├── hg19.binned.bed
| │ | ├── hg19.chrom.sizes
| │ | ├── hg19.fa
| │ | ├── hg19.fa.fai
| │ | ├── hg19.fa.gz
| │ | ├── hg19.GCpt.bedGraph
| │ | ├── hg19.GCpt.tss.bedGraph
| │ | ├── hg19.refGene.gtf.gz
| │ | └── hg19.tss.bed
| │ ├── Normal_chr_pc_selected.txt
| │ ├── Normal_clus.txt
| │ ├── Normal_cor.txt
| │ ├── Normal_mapQ15_50kb_pca
| │ | └── intra_pca
| │ | └── Normal_mapQ15_50kb_mat
| │ | ├── chr1.bed
| │ | ├── chr1.cmat.txt
| │ | ├── chr1.distparam
| │ | ├── chr1.PC1.bedGraph
| │ | ├── chr1.PC2.bedGraph
| │ | ├── chr1.pc.bedGraph
| │ | ├── chr1.pc.txt
| │ | ├── chr1.precmat.txt
| │ | ├── chr1.svd.rds
| │ | ├── chr1.txt
| │ | └── ...
| │ ├── Normal_vals.txt
| │ ├── Tumor_chr_pc_selected.txt
| │ ├── Tumor_clus.txt
| │ ├── Tumor_cor.txt
| │ ├── Tumor_mapQ15_50kb_pca
| │ | └── intra_pca
| │ | └── Tumor_mapQ15_50kb_mat
| │ | ├── chr1.bed
| │ | ├── chr1.cmat.txt
| │ | ├── chr1.distparam
| │ | ├── chr1.PC1.bedGraph
| │ | ├── chr1.PC2.bedGraph
| │ | ├── chr1.pc.bedGraph
| │ | ├── chr1.pc.txt
| │ | ├── chr1.precmat.txt
| │ | ├── chr1.svd.rds
| │ | ├── chr1.txt
| │ | └── ...
| │ └── Tumor_vals.txt
| └── 50kb_resolution
|
├── G_Differential_contacts_analyses_SELFISH
| ├── log
| └── Normal_vs_Tumor
| ├── Normal_vs_Tumor_50kb_SELFISH.txt
| └── Normal_vs_Tumor_100kb_SELFISH.txt
|
└── H_Stripes_analyses_STRIPPEN
├── Normal
| ├── logs
| ├── Normal_50kb
| | ├── result_filtered.tsvstripenn.log
| | ├── result_unfiltered.tsv
| | └── stripenn.log
| ├── Normal_100kb
| └── ...
└── ...