epigenomics

Epigenomics

ATAC-seq and ChIP-seq analysis for chromatin accessibility and transcription factor binding. Covers the filtering that precedes peak calling, ATAC-specific peak calling, differential binding and the DiffBind 3.x changes that silently alter results, motif enrichment, TF activity from accessibility, and assigning peaks to genes without pretending distance is regulation.

When to Use This Skill

Activate when the user requests:

• ATAC-seq or ChIP-seq peak calling, or MACS
• Differential accessibility or differential binding
• Motif enrichment, TF footprinting, or chromVAR
• Assigning peaks to genes, or enhancer-promoter linking
• Integrating accessibility or binding with expression
• Chromatin QC: FRiP, TSS enrichment, fragment size distribution

Inputs

Data Type	Form	Note
Aligned reads	BAM, duplicates marked	ATAC needs chrM and blacklist removal first
Peaks	narrowPeak / broadPeak	narrow for TF and ATAC, broad for most histone marks
Sample sheet	CSV with condition, replicate, bamReads, peaks	DiffBind's entry point
Genome annotation	TxDb or GTF	for TSS enrichment and peak annotation
Motif database	JASPAR	version changes the answer

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Environment

Versions verified 2026-08.

pip install MACS3          # 3.0.4  peak calling
pip install deeptools      # 3.5.6  coverage, matrices, QC plots

BiocManager::install(c("DiffBind",     # 3.22.2  differential binding
                       "csaw",         # 1.46.0  window-based differential
                       "chromVAR",     # 1.34.1  TF activity from accessibility
                       "ChIPseeker",   # 1.48.0  peak annotation
                       "motifmatchr",  # 1.34.0  motif scanning
                       "TFBSTools",    # 1.50.0
                       "JASPAR2024",   # motif database
                       "rGREAT"))      # 2.14.0  regulatory region enrichment

Use MACS3 (3.0.4, released 2026-02), not MACS2. MACS2's last release was
2023-07 and development moved to MACS3, which is actively maintained. Most
tutorials still say macs2; the command is macs3 and the options differ in
places.

JASPAR2024 is the latest Bioconductor release; JASPAR2026 does not exist.
Record which JASPAR version you used, because motif matrices are revised
between releases and enrichment results move with them.