peak-calling

What problem does it solve?

Automates peak calling from BAM files for ChIP-seq and ATAC-seq experiments.

Core Features & Use Cases

• Automatic experiment recognition and peak calling with MACS3 based on the BAM files in the current directory.
• Dynamic parameter selection with user prompts for genome size and q-value, and required control files for ChIP-seq data.
• Automatic detection of sequencing type (single- or paired-end) and peak mode (narrow or broad), and use of filtered BAM when available.
• Output structure includes peaks, logs, and a parameter log detailing the chosen options.
• Supports ATAC-seq with specialized parameters and produces a reproducible results trail.

Quick Start

Run the peak-calling skill in a project directory containing BAM files to automatically generate peak calls and logs.