This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

  • FastQC - Raw read QC
  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution
  • genome - The genome related files used in the pipeline.
  • bwa - The alignments of trimmed reads.
  • pairs - The interaction pairs and their quality control reports.
  • Matrix for visualization - Cooler or Juicer files for visualization
  • ATACpeak - The peaks called for ATAC reads (R2 reads).
  • A/B Compartments - Called A/B compartments.
  • TADs - Called topologically associating domains.
  • Interactions - The chromatin interactions determined by MAPS/HiCDCPlus or other tools.
  • DifferentialAnalyis - Differential analysis for chromatin interactions.
  • Annotation - Annotations for the interactions.
  • fragmentPeak - The peaks called for R1 reads.
  • HiCARpeak - The high resolution loops called for R1 and R2 peaks for motif analysis.
  • TFEA - The motif enrichment analysis results.
  • circos - The circos plots.
  • V4C - The virtual 4C plots.
  • APA - The aggregate peak analysis results.
  • igv.js - The track files which can be viewed by web-server.


Output files
  • fastqc/
    • *_fastqc.html: FastQC report containing quality metrics.
    • * Zip archive containing the FastQC report, tab-delimited data file and plot images.

FastQC gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the FastQC help pages.

MultiQC - FastQC sequence counts plot

MultiQC - FastQC mean quality scores plot

MultiQC - FastQC adapter content plot

NB: The FastQC plots displayed in the MultiQC report shows untrimmed reads. They may contain adapter sequence and potentially regions with low quality.


Output files
  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see

Pipeline information

Output files
  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter’s are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.


Output files
  • genome/
    • genome.fa.sizes: chromosome sizes file
    • genome.fa.fai: genome index file
    • filtered/genome.include_regions.bed: filtered genome by blacklist
    • digest/*: genomic features files digested by given restriction enzyme

If the mappability file is not provided in the profile file, the GenMap will be used to create the mappability file with read length set to 50.


Output files
  • bwa/mapped/bam/*.(bam|bai): The files resulting from the alignment of individual libraries will contain the coordinate sorted alignment files in *.bam format.
  • bwa/mapped/QC/*: The stats of mapping results.

Adapter-trimmed reads are mapped to the reference assembly using BWA::mem. A genome index is required to run BWA so if this is not provided explicitly using the --bwa_index parameter then it will be created automatically from the genome fasta input. The index creation process can take a while for larger genomes.


Output files
  • pairs/
    • raw/*: The raw reads pairs for each sample and stats for the pairs.
    • filtered/*: The filtered files in hdf5 format. The hdf5 files in the folder can be used to generate virtual 4C plots.
    • QC/*: The quality analysis results.

The raw and filtered pairs exported by pairtools. The quality analysis for filtered pairs were done by pairsqc.

The hdf5 filtered pairs contains following groups:

  • header/, including total reads, chromosome name and sizes, tile width for index.
    • header/chrom_sizes, COMPOUND
    • header/header, STRING
    • header/tile_width, INTEGER
    • header/total, INTEGER
  • data/, pairs in path data/chr1_for_R1_reads/chr2_for_R2_reads/tileIndex1_tileIndex2/, the tile index is calculated by the ceiling of posistion divided by tile width.
    • position, genomic location saved in path data/chr1/chr2/tileIndex1_tileIndex2/position
    • strand, strand info saved in path data/chr1/chr2/tileIndex1_tileIndex2/strand

Matrix for visualization

Output files
  • matrix/mcool/*: The mcool files for each group.
  • matrix/hic/*: The .hic files for each group.
  • matrix/HiCExplorer/*: The h5 files normalized by HiCExplorer for each group.

Cooler files for visualization. To view the .mcool files, you may want to try higlass-manage. Once higlass-manage is installed, view the files using the command:

higlass-manage view cooler/mcool/your.mcool

Juicebox can be used to view the .hic file. Visualizing the .hic file with Juicebox is an alternative when higlass-manage is not available.

Call peaks for R2 reads

Output files
  • atac_peak/
    • R2_bigwig/*: The bigWig files of R2_reads.
    • peaks_per_Group/*: The called peaks for each group.
    • merged_peaks/*: The merged peaks for all groups.
    • QC/*: The quality controls

The peaks called ATAC reads (R2 reads) by MACS2. Different from ATAC-seq peak calling, the ATAC reads in HiCAR is single end. By default, the peaks are called by --no-model parameter for the R2 reads in BED format.


Output files
  • compartments
    • cooltools/
      • *: The tables and bigwig files of A/B compartments.
    • homer/
      • pca/*: The Principal Component Analysis outputs.
      • compartments/*: The called A/B compartments.
    • HiCExplorer/
      • *: By default, all intermediate matrices will be generated: obs_exp-all.h5, pearson_all.h5 and covariance_all.h5.

To compute the A/B compartments ask correlation matrix computed by observed/expected matrix in the way described by Lieberman-Aiden and are determined by the eigenvectors based on the covariance matrix of the correlation matrix.


Output files
  • tads
    • cooltools/
      • *: The called TADs.
    • homer/
      • *_tagdir/*: The called TAD in BED format.
    • HiCExplorer/
      • *: The output form hicFindTADs:
        • *_hicfindtads_tad_score.bam: the TAD-separation score file
        • * the z-score matrix
        • *_hicfindtads_boundaries.bed: the bed files with the boundary location
        • *_hicfindtads_domains.bed: the bed files with the domains
        • *_hicfindtads_score.bedgraph: the bedgraph file with the TAD-score that can be visualized in a genome browser.

To call TADs by HiCExplorer, a corrected matrix is needed. The TAD-separation score is based on a Z-score matrix for all bins. The TAD-separation score and the matrix will be visualized using hicPlotTADs.

Chromatin interactions

Output files
  • interactions
    • hicdcplus/
      • merged/*: The merged loops for each resolution.
      • *: The tables of chromatin interactions with p-value and fdr.
    • maps/
      • merged/*: The merged loops for each resolution.
      • *: The tables of chromatin interactions with p-value and fdr.
    • peakachu/
      • merged/*: The merged loops for each resolution.
      • *: The bedpe files of chromatin interactions with peakachu scores.

Use different caller to call chromatin loops/interactions can be done by set the parameter --interactions_tool in command line or interactions_tool in the configuration file.

The default chromatin interactions are called by MAPS. MAPS is a model-based analysis of long-range chromatin interactions for AND or XOR reads.

  • AND set: bin pairs with both ends overlapping two anchors of interaction.
  • XOR set: bin pairs with one end overlapping one anchor of the interaction.

It will remove the systematic bias by accessibility. By default, the interactions are called by positive poisson regression model and then filtered by coverage (default is 12 per bin), fold change (default is 2 times over expected value) and fdr (default is 0.01).

The chromatin interactions called by HiCDCPlus and peakachu or other tools are also located in interactions folder.

Differential analysis

Output files
  • differential_analysis/<differential analysis tool>/<interaction caller>/*: Differential analysis results.

Differential analysis for the loops by edgeR, diffHic or simply set operation will be put in the folder. The subfolder names are the tools used in differential analysis and in each subfolder, different resolution results will be saved in another subfolder.

The input counts are filtered counts dumped by pairtools for each samples. The differential analysis is done for validated chromatin interactions by loop caller.


Output files
  • annotations/<interaction caller>/*: Annotation results.

Annotation is done by ChIPpeakAnno for the overlap features (gene level) or nearest features.

Call peaks for fragment reads

Output files
  • fragment_peak/
    • R1_bigwig/
      • byGroup/*: The bigWig files of R1_reads for each group.
      • pos1/*: The bigWig files of 5’ ends of R1_reads.
    • merged_peaks/merged_peak.bed: The bed file with merged R1 peaks from all samples.
    • peaks_per_Group/*: The MACS2 output for each group.

The peaks called fragment (R1) reads by fitting the reads counts in fragmentation sites with Poisson distribution. The fragment reads will be more noisy compare to ATAC (R2) reads and the p value cutoff will be higher to get proper peaks for interaction calling.

High resolution interactions

Output files
  • high_peak
    • */: The high resolution interactions in bedpe format and tab delimited format.

The HiCAR fastq files are paired ends (PE). But it will be difficult to check the reads in pairs for IGV. In order to view the reads located in the R1 and R2 peaks, the psuedo-bam files are created by adding insertion to the PE and converted as single ends. When the psuedo-bam file is load to IGV, the PEs will be linked by a line, which will help user to double check the reads located in the chromation interactions. The high resolution chromatin interactions (HiPeak) are called by similar methods like MAPS to remove the systematic bias by accessibility. The difference is that HiPeak will also consider the trans-interactions. The output of HiPeak is designed for motif enrichment analysis.

Motif enrichment

Output files
  • tfea/<package_name>/<tool_name>/*: transcription factor enrichment analysis results.

The TFEA will be done for the peaks call by R1, R2 reads and the high resolution interactions.


Output files
  • circos/*: circos plots.

circos is a perl package for visualizing data in a circular layout. circos is used to produce the genomic view of chromatin interactions for HiPeak.

Virtual 4C

Output files
  • v4c/<package_name>/*: Virtual 4C plots.

The default events are differential results top events.

Aggregate peak analysis

Output files
  • apa/<package_name>/*: Aggregate peak analysis plots.


Output files
  • igv.js/*: index.html, readme.txt and track_files.txt.

The track.txt contain the reads tracks and interactions called by MAPS. Copy all the files into a web-server to view the data vis igv.js.