Individual skill

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, and nucleosome-free fragment selection. 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.

skills/pipeline-atacseq/SKILL.md

Source commit 36836c8725fd4d20d9c851ce314f5151aea5f57c

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Observed behavior

Network or broad shell

Last checked

Nov 6, 2026

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