gDNAx

gDNAx provides diagnostics for assessing genomic DNA contamination in RNA-seq data, generates plots representing these diagnostics, determines strand library protocol and strandedness, and filters out reads of potential gDNA origin.

Key Features:

• gDNA Contamination Diagnostics: Assesses genomic DNA contamination in RNA-seq data and generates diagnostic plots.
• Strand Library Protocol Inference: Provides insight into the strand library protocol used for sequencing.
• Strandedness Determination: Determines the strandedness of data in the case of strand-specific libraries.
• gDNA Read Filtering: Filters out reads of potential genomic DNA origin from RNA-seq data.

Scientific Applications:

• RNA-seq Quality Control: Evaluates and visualizes genomic DNA contamination in RNA-seq datasets to ensure data integrity.
• Strand-Specific Library Validation: Identifies the strand library protocol and confirms correct strandedness assignment in strand-specific RNA-seq experiments.
• Contaminant Removal: Enables removal of reads derived from genomic DNA to improve downstream RNA-seq analysis accuracy.

Methodology:

The package analyzes RNA-seq data to detect genomic DNA contamination, infer strand library protocol, determine strandedness for strand-specific libraries, and filter reads of potential gDNA origin.