pipeline-chipseq
Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.
npx skills add majiayu000/claude-skill-registry --skill pipeline-chipseq --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# ENCODE ChIP-seq Pipeline ## When to Use - User wants to run a ChIP-seq processing pipeline from FASTQ to peaks and signal tracks - User asks about "ChIP-seq pipeline", "MACS2", "peak calling", "BWA alignment for ChIP", or "IDR" - User needs to process histone or TF ChIP-seq data following ENCODE standards - Example queries: "process my ChIP-seq FASTQs", "run the ENCODE ChIP-seq pipeline", "call peaks from ChIP-seq with MACS2 and IDR" Execute the ENCODE ChIP-seq processing pipeline from raw FASTQ files through peak calling, IDR analysis, and signal track generation. This skill provides a complete Nextflow DSL2 implementation following ENCODE uniform analysis standards. ## Overview The ENCODE ChIP-seq pipeline processes chromatin immunoprecipitation sequencing data through a series of well-defined stages: quality control, adapter trimming, alignment to a reference genome, filtering and deduplication, peak calling with MACS2, replicate consistency analysis via IDR, and signal track generation. Each stage is parameterized according to ENCODE standards and produces QC metrics for comprehensive quality assessment. This pipeline handles both transcription factor (TF) ChIP-seq and histon
- When to Use
- Overview
- Key Literature
- Pipeline Stages
- Stage Summary
- Input Requirements
- Required Files
- Sample Sheet Format
- Narrow vs Broad Peak Mode Decision
- QC Thresholds
- Interpreting QC: Traffic Light System
- Execution
- Quick Start (Local Docker)
- SLURM HPC
nextflow run scripts/main.nf \ nextflow run pipeline-chipseq/main.nf \
What does the pipeline-chipseq skill do?
Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill pipeline-chipseq --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.