bio-workflows-chipseq-pipeline

What problem does it solve?

ChIP-seq data analysis pipeline that takes raw FASTQ files through QC, alignment, peak calling with MACS3, and annotation with ChIPseeker, delivering annotated peaks and QC metrics.

Core Features & Use Cases

• End-to-end ChIP-seq workflow covering QC, alignment, deduplication, peak calling with MACS3, and annotation with ChIPseeker.
• Supports narrow and broad peaks, suitable for TFs and histone marks, with FRiP QC checks.
• Use Case: A researcher processes two IP replicates and two Input controls to obtain annotated peaks and a reproducible report.

Quick Start

Run the end-to-end ChIP-seq workflow on your IP and Input FASTQ samples to generate annotated peaks and QC metrics.