chipseq

What problem does it solve?

This Skill turns raw ChIP-seq sequencing inputs into a reproducible, validated analysis run with peak calling, QC, and downstream reporting, so researchers do not have to remember dozens of pipeline flags.

Core Features & Use Cases

• Samplesheet-driven execution: Uses a structured CSV input and required reference FASTA to launch the pipeline correctly.
• Full ChIP-seq workflow coverage: Supports alignment, peak calling, consensus peaks, QC, and differential analysis across common nf-core options.
• Controlled parameter selection: Exposes documented parameter groups, allowed values, and constraints for safer automated runs.
• Use case: A researcher can point the Skill at a prepared samplesheet, select the proper aligner and genome reference, and generate publishable outputs and MultiQC reports in one run.

Quick Start

Ask the assistant to run the chipseq Skill on my samplesheet and FASTA reference and save the results to my chosen output directory.