FADU

FADU quantifies prokaryotic gene expression from RNA sequencing (RNA-Seq) data by assigning fragment counts proportionally to overlapping genomic features to improve accuracy for operonic and polycistronic transcripts.

Key Features:

• Proportional Count Assignment: Assigns partial counts proportional to the length of the fragment overlapping each target feature to enable more accurate gene-level quantification within operons.
• Handling Ambiguous Multigene Fragments: Allocates counts for fragments that overlap multiple genes proportionally to minimize misassignment among multigene regions.
• Operon-aware Quantification: Specifically addresses quantification challenges in prokaryotic genomes that often lack well-annotated full-length transcripts and untranslated regions (UTRs).
• Performance Evaluation: Benchmarked against eXpress, featureCounts, HTSeq, kallisto, and Salmon using paired-end datasets from Ehrlichia chaffeensis, Escherichia coli, and the Wolbachia endosymbiont wBm, demonstrating improved accuracy for operonic genes.

Scientific Applications:

• Prokaryotic Transcriptome Quantification: Quantifies gene-level expression in bacteria and other prokaryotes, including those with polycistronic transcripts.
• Operon Expression Analysis: Provides accurate expression estimates for genes located within operons and other multigene transcriptional units.
• Microbial Physiology, Pathogenesis, and Symbiosis Studies: Supports investigations into microbial physiology, pathogenesis, and symbiotic relationships by improving reliability of gene expression measurements.

Methodology:

Computes partial counts proportional to fragment-feature overlap, resolves multigene fragment ambiguity by proportional allocation, and was benchmarked against eXpress, featureCounts, HTSeq, kallisto, and Salmon on paired-end RNA-Seq datasets from Ehrlichia chaffeensis, Escherichia coli, and Wolbachia wBm.