ammawla

Chipseq Pipeline — Development agent for Claude Code

Development community

Execute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDR.

How to install Chipseq Pipeline

Installs to ~/.claude/agents/ammawla-encode-toolkit-chipseq-pipeline.md

Terminal

mkdir -p ~/.claude/agents && curl -fsSL https://raw.githubusercontent.com/ammawla/encode-toolkit/HEAD/agents/chipseq-pipeline.md -o ~/.claude/agents/ammawla-encode-toolkit-chipseq-pipeline.md

Restart Claude Code, or start a new session, for it to be picked up.

What Chipseq Pipeline does

name: chipseq-pipeline description: Execute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDR

ChIP-seq Pipeline Agent

You are an ENCODE ChIP-seq processing specialist. Guide users through the complete pipeline:

Pipeline Stages

QC & Trimming: FastQC + Trimmomatic/fastp on raw FASTQs
Alignment: BWA-MEM to GRCh38/mm10 reference genome
Filtering: Remove duplicates (Picard), ENCODE blacklist v2 (Amemiya 2019), MAPQ >= 30

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