ChIP-seq & ATAC-seq Reporting Tool

Last Modified: 2026-06-09

Authors: Pauline Hughes, Gerardo Zapata

Generates a client-ready HTML report and results archive from GenPipes' ChIP-seq pipeline output, for both ChIP-seq and ATAC-seq data.

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Installation

git clone https://github.com/GerardoZA/ChIP_Reporting.git

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Requirements

GenPipes chipseq steps must be completed before running:

Data type	Required steps
ChIP-seq	1 (if needed), 2–18, 20–21
ATAC-seq	1 (if needed), 2–18, 20–21 (with -t atacseq)

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How to Run

Navigate to the GenPipes chipseq report/ output directory, then submit to SLURM:

genpipes_chipseq_report (standard)

sbatch path/to/repo/ChIP_Reporting/genpipes_chipseq_report/generate_report.sh "Project ID" "Primary Contact" ["atacseq"]

[ARG3] is optional.

genpipes_chipseq_report_with_wrapper (advanced)

Allows specifying a custom ini file, readset file, and start date.

Option 1 — direct submission:

sbatch path/to/genpipes_chipseq_report_with_wrapper/generate_report.sh \
  "Project ID" "Primary Contact" "chipseq" \
  "ChipSeq.chipseq.2025-08-11T15.44.04.config.trace.ini" \
  "myReadset.tsv" "2025-08-26"

Option 2 — interactive wrapper (login node):

bash path/to/genpipes_chipseq_report_with_wrapper/generate_report_wrapper.sh

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Output

A tarball (GenPipes_ChIP-seq_Results.tar.gz or GenPipes_ATAC-seq_Results.tar.gz) containing:

• ChIP-seq_Report.html or ATAC-seq_Report.html
• annotations/ — HOMER motif results (ChIP-seq only)
• peak_call/ - MACS2 peaks called
• graphs/ — fingerprint plots, read coverage PCA, insert size plots (ATAC-seq only)
• IHEC_*_metrics_AllSamples.tsv
• *.multiqc.html
• tracks_bigWigs.zip
• trimReadsetTable.tsv