ATAC-seq Quality Control

About

Automate the quality control process for chromatin accessibility experiments with specialized biological validation tools. This skill processes filtered BAM and peak files to compute critical metrics such as Transcription Start Site (TSS) enrichment scores, nucleosome banding patterns, and the Fraction of Reads in Peaks (FRiP). By leveraging the ataqv framework, it helps researchers ensure their sequencing data meets rigorous biological standards, providing both interactive HTML reports and structured JSON metrics for downstream epigenomic analysis.

Key Features

• Calculates TSS enrichment scores to assess library signal-to-noise ratios
• 2 GitHub stars
• Computes Fraction of Reads in Peaks (FRiP) for library validation
• Generates interactive HTML reports and structured JSON metrics via ataqv
• Analyzes fragment size distributions for nucleosome periodicity
• Automates reference file generation tailored to specific genome assemblies

Use Cases

• Assessing the quality of ATAC-seq libraries post-alignment and peak calling
• Identifying low-quality samples based on chromatin-specific biological metrics
• Standardizing QC reporting across multiple genomic samples and assemblies