pipeline-chipseq

What problem does it solve?

This Skill streamlines the end-to-end processing of ChIP-seq data, ensuring high-quality, reproducible peak calling aligned with ENCODE standards.

Core Features & Use Cases

• Data Processing: Runs quality control, alignment, filtering, deduplication, and peak calling on ChIP-seq datasets.
• Reproducibility & QC: Implements IDR analysis, computes QC metrics (FRiP, NSC, RSC, NRF), and provides comprehensive reports.
• Use Case: Researchers can process raw FASTQ files from experimental outputs to generate reliable peak datasets for downstream functional annotation or comparative analysis.

Quick Start

Process your ChIP-seq FASTQ files by specifying input files, genome assembly, and peak mode (narrow or broad) in a single command with the appropriate profile.