pipeline-atacseq

What problem does it solve?

This Skill streamlines the analysis of ATAC-seq data by providing an automated pipeline from raw sequencing reads to high-confidence accessible chromatin peaks, enabling accurate epigenomic insights.

Core Features & Use Cases

• Data Processing: Performs quality control, adapter trimming, alignment, and Tn5 offset correction on raw FASTQ files.
• Peak Identification: Calls peaks on nucleosome-free fragments to identify open chromatin regions, suitable for TF binding analysis.
• QC & Visualization: Provides comprehensive quality metrics including TSS enrichment, fragment size distributions, and signal tracks for downstream interpretation or publication.
• Use Case: Researchers analyzing ENCODE ATAC-seq datasets or their own samples can utilize this pipeline to generate reproducible, publication-ready accessibility maps aligned with ENCODE standards.

Quick Start

Run the pipeline with your FASTQ files and reference genome to obtain peaks and QC reports for chromatin accessibility studies.