MACS2

MACS2, short for Model-based Analysis of ChIP-Seq 2, is a widely used software tool for peak calling in ChIP-Seq, ATAC-Seq, and related sequencing assays. It improves the identification of enriched regions representing protein-DNA interactions by modeling fragment size and local biases, making it suitable for both transcription factor binding (narrow peaks) and histone modification signals (broader peaks).

MACS2 is open-source and implemented in Python. It is distributed on the project's repository and is released under the MIT license. The program can use treatment/control input samples to reduce background noise and artifacts, enhancing specificity. It supports calling both narrow peaks and broad peaks, with options tailored to different data types, including ATAC-Seq and DNase-Seq alongside traditional ChIP-Seq.

Input to MACS2 typically consists of aligned reads in BAM (or similar) formats, with optional control samples. It outputs peak lists in formats such as narrowPeak and broadPeak, which contain coordinates, significance metrics (p-values and q-values), peak summits, and associated scores. The tool can also generate signal tracks or bedGraph data for downstream visualization and analysis.

Common usage involves a command-line invocation such as macs2 callpeak with parameters for input files, genome size, and output location. Users may specify options to control peak shape estimation, such as --nomodel or --shift and --extsize, and to adjust stringency with -q or -p. MACS2 is compatible with standard downstream analysis workflows and is frequently integrated with annotation, motif discovery, and visualization steps.

Limitations include reliance on sequencing depth and quality, potential false positives if controls are inadequate, and varying performance for broad versus narrow chromatin features. Proper experimental design, replicates, and quality control remain important for reliable peak calling.