dupRadar

dupRadar assesses per-gene PCR duplicate rates in RNA-Seq data to distinguish PCR clonal artifacts arising during NGS library preparation from natural read duplication driven by gene expression.

Key Features:

• Per-gene duplicate assessment: Calculates the fraction of duplicate reads on a per-gene basis.
• Expression-aware discrimination: Relates per-gene duplication levels to gene expression to separate natural over-sequencing of highly expressed genes from technical duplicates.
• PCR artifact detection: Identifies deviations in duplication patterns indicative of PCR clonal artifacts introduced during library preparation.
• Gene-specific versus global metrics: Provides gene-level duplication metrics that complement or supersede global duplication rate summaries.
• Relevance to low-input and single-cell data: Targets quality control issues that are particularly important for low-input and single-cell RNA-Seq datasets.

Scientific Applications:

• RNA-Seq quality control: Evaluates duplicate-read composition as a QC metric for RNA-Seq experiments.
• Detection of library/preparation artifacts: Detects PCR-induced duplication artifacts in NGS libraries.
• Assessment of low-input and single-cell experiments: Assesses duplicate fractions where limited input increases the risk of amplification artifacts.

Methodology:

Computes per-gene duplicate read fractions and compares them to gene expression levels to distinguish PCR-induced duplicates from expression-driven read duplication.