ChIP-seq Biological Quality Control

概要

Provides a comprehensive quality control pipeline specifically designed for protein-binding assays like ChIP-seq. It automates the calculation of essential metrics such as Normalized Strand Cross-correlation (NSC), Relative Strand Cross-correlation (RSC), and Fraction of Reads in Peaks (FRiP) using aligned BAM files and peak call data. This skill is ideal for researchers needing to validate the signal-to-noise ratio and enrichment quality of their ChIP experiments after filtering and peak calling.

主な機能

• Supports multiple peak file formats including narrowPeak and broadPeak
• Automates project directory initialization and standardized output management
• 2 GitHub stars
• Computes Fraction of Reads in Peaks (FRiP) for enrichment validation
• Calculates strand cross-correlation metrics (NSC and RSC)
• Generates cross-correlation visualization plots for visual inspection

ユースケース

• Generating standardized QC metrics for biological replication analysis
• Validating ChIP-seq data quality after alignment and peak calling
• Evaluating the enrichment quality of protein-DNA binding assays