chip-seq

What problem does it solve?

Automates end-to-end ChIP-seq analysis, including QC, peak calling, annotation, motif analysis, and differential binding interpretation to streamline workflow and ensure reproducibility.

Core Features & Use Cases

• QC-focused checks for mapping quality, duplication rate, FRiP, and replicate concordance to ensure data reliability.
• Peak calling with MACS3 for narrow or broad marks, with signal track export and browser-ready tracks.
• Peak annotation to promoters, gene bodies, and regulatory elements, plus downstream interpretation of motifs and differential binding.
• Exportable tracks and summaries suitable for genome browsers and reports, with ready-to-use outputs for downstream analyses.
• Use cases include TF ChIP-seq and histone mark ChIP with or without input controls, in multi-replicate designs.

Quick Start

Run the ChIP-seq workflow on your chip.bam with an optional input.bam to generate peaks, annotations, motifs, and browser tracks.