macs3-peak-calling

What problem does it solve?

This Skill automates the identification of significant genomic regions (peaks) from ChIP-seq and ATAC-seq experiments, crucial for understanding where proteins bind or chromatin is accessible.

Core Features & Use Cases

• Peak Calling: Differentiates between narrow peaks (for transcription factors) and broad peaks (for histone modifications).
• Signal Tracks: Generates visualization-ready signal tracks (bedGraph, bigWig) for genome browsers.
• Use Case: Analyze ChIP-seq data to pinpoint transcription factor binding sites across the genome, or identify open chromatin regions in ATAC-seq experiments for further functional analysis.

Quick Start

Call narrow peaks from 'chip.bam' using 'input.bam' as control, with a q-value threshold of 0.05.