pipeline-cutandrun

What problem does it solve?

This Skill automates the complex workflow of processing CUT&RUN and CUT&Tag sequencing data to identify genomic binding sites accurately and efficiently.

Core Features & Use Cases

• End-to-End Processing: Automates from raw FASTQ files through alignment, filtering, spike-in normalization, peak calling, and signal track generation.
• Specialized Peak Calling: Uses SEACR for low-background CUT&RUN and CUT&Tag data, with optional MACS2 comparison for validation.
• Use Case: Researchers can process small-scale chromatin profiling experiments targeting specific histone marks or transcription factors, with outputs suitable for downstream annotation and visualization.

Quick Start

Specify your FASTQ files, reference genomes, and parameters to run the pipeline on your CUT&RUN data for rapid peak detection and normalization.