plugin/skills/pipeline-cutandrun

What problem does it solve?

This Skill enables efficient processing of CUT&RUN and CUT&Tag sequencing data to identify precise protein-DNA interactions, significantly reducing manual analysis time and improving result accuracy.

Core Features & Use Cases

• End-to-End Workflow: From FASTQ input through alignment, spike-in normalization, peak calling, and QC.
• Library Preparation Optimization: Recommends parameters based on target type and experimental setup.
• Use Case: Researchers analyzing transcription factor binding sites can process their CUT&RUN data to obtain high-confidence peak sets with spike-in calibration, fitting into broader epigenomic studies.

Quick Start

Run the pipeline with your paired-end FASTQ files specified, selecting appropriate parameters for your genome and spike-in reference to generate peak calls and QC metrics.