Differential ChIP-seq Peak Calling — Comparative Chromatin Binding Analysis

Differential ChIP-seq peak calling identifies genomic loci where a protein of interest — typically a transcription factor or histone mark — shows significantly altered binding or occupancy between two or more biological conditions. By combining standard ChIP-seq peak detection with count-based statistical testing, the method reveals condition-specific regulatory elements, providing a genome-wide map of dynamic chromatin interactions underlying cellular state changes.