pipeline-atacseq
Execute ENCODE ATAC-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. Handles Tn5 transposase offset correction, mitochondrial read removal, nucleosome-free fragment selection, and TSS enrichment scoring. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS enrichment.
npx skills add majiayu000/claude-skill-registry --skill pipeline-atacseq-ammawla-encode-toolkit --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 ATAC-seq Pipeline ## When to Use - User wants to run an ATAC-seq processing pipeline from FASTQ to peaks and signal tracks - User asks about "ATAC-seq pipeline", "Tn5 shift", "chromatin accessibility pipeline", or "Bowtie2 for ATAC" - User needs to process ATAC-seq data with proper Tn5 insertion site correction - Example queries: "process my ATAC-seq FASTQs", "run ENCODE ATAC-seq pipeline", "call accessibility peaks from ATAC-seq" Execute the ENCODE ATAC-seq processing pipeline from raw FASTQ files through Tn5 offset correction, peak calling, IDR analysis, and signal track generation. This skill provides a complete Nextflow DSL2 implementation following ENCODE uniform analysis standards. ## Overview ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) uses the Tn5 transposase to probe open chromatin regions. The ENCODE pipeline processes ATAC-seq data through quality control, alignment with Bowtie2, Tn5 insertion site correction (+4/-5 bp offset), mitochondrial read removal, nucleosome-free fragment selection, peak calling with MACS2, and IDR-based replicate consistency analysis. Key differences from ChIP-seq: Bowtie2 aligner (optimized for short fragment
- When to Use
- Overview
- Key Literature
- Pipeline Stages
- Stage Summary
- Input Requirements
- Required Files
- Sample Sheet Format
- Tn5 Transposase Offset Correction
- Fragment Size Distribution
- QC Thresholds
- TSS Enrichment Score
- Execution
- Quick Start (Local Docker)
nextflow run scripts/main.nf \ nextflow run pipeline-atacseq/main.nf \
What does the pipeline-atacseq skill do?
Execute ENCODE ATAC-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. Handles Tn5 transposase offset correction, mitochondrial read removal, nucleosome-free fragment selection, and TSS enrichment scoring. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS enrichment.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill pipeline-atacseq-ammawla-encode-toolkit --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.