CleanUpRNAseq

CleanUpRNAseq detects and corrects genomic DNA contamination in RNA-seq data to reduce false discovery rates in differential gene expression analysis.

Key Features:

• gDNA Contamination Detection: Checks RNA-seq data for genomic DNA contamination arising from library preparation methods such as rRNA-depletion and SMART-seq when DNase I digestion is improperly performed.
• Correction Methods for Unstranded Data: Offers three correction methods specifically for unstranded RNA-seq data.
• Correction Method for Stranded Data: Provides a dedicated correction approach for stranded RNA-seq data.
• Post-Alignment Quality Assessment: Serves as a tool for quality assessment after read alignment in RNA-seq workflows.

Scientific Applications:

• Differential Expression Analysis: Reduces false discovery rate of differentially expressed genes by correcting gDNA-contaminated RNA-seq data.
• Gene Expression Quantification: Improves accuracy of gene expression quantification when integrated into RNA-seq analysis workflows such as OneStopRNAseq.
• Low-Input Sample Analysis: Enables identification and correction of gDNA contamination in scarce and invaluable RNA samples to maximize data utility.

Methodology:

CleanUpRNAseq performs post-alignment analysis of RNA-seq data; validation was performed on published RNA-seq datasets with known levels of gDNA contamination and real-world RNA-seq data across diverse library protocols.