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encode/ATAC-seq Pipeline

Published Demo
H. sapiens ATAC-seq Epigenomics Updated 3 days ago
This is a demo page showing what a space detail page looks like on Cyanea. The content shown is illustrative.

End-to-end ATAC-seq analysis with QC reports — from FASTQ to peak calls.

A production-grade ATAC-seq analysis pipeline following ENCODE best practices. This space bundles analysis notebooks, reference datasets, and quality control protocols into a single reproducible workspace.

Pipeline steps

  1. Read QC — adapter trimming, quality filtering with fastp
  2. Alignment — Bowtie2 alignment to GRCh38 with mitochondrial read filtering
  3. Post-alignment QC — duplicate marking, fragment size distribution, TSS enrichment
  4. Peak calling — MACS2 narrow peak calling with IDR for replicate consistency
  5. Signal tracks — normalized bigWig generation for genome browser visualization
  6. Differential accessibility — DESeq2-based differential analysis between conditions

Quality metrics

Every run produces a comprehensive HTML QC report including library complexity estimates, TSS enrichment scores, FRiP values, and reproducibility metrics (IDR).

Contents

6 Notebooks
4 Datasets
2 Protocols

Compliance

FAIR Gold Reproducible

Tags

ATAC-seq chromatin accessibility pipeline epigenomics peak calling