baerhunter

baerhunter identifies and annotates expressed non-coding RNAs and untranslated regions (UTRs) from bacterial RNA-seq reads mapped to a reference genome to enable more comprehensive bacterial transcriptome analyses.

Key Features:

• R package implementation: Implemented as an R package for integration into RNA-seq analysis workflows.
• Coverage-based discovery: Uses a coverage-based method to detect expressed non-coding RNAs and UTRs from mapped RNA-seq reads.
• Prediction and annotation: Predicts and annotates expressed intergenic regions to complement incomplete genome annotations.
• Expression-based filtering: Provides filtering options to refine feature selection based on expression strength.
• Transcript abundance quantification: Quantifies transcript abundance for detected coding and non-coding features.
• Differential gene expression testing: Performs differential expression testing on identified transcripts.
• Benchmarking: Demonstrated favorable performance in comparative evaluations using simulated and real data.

Scientific Applications:

• Small RNA discovery: Identification and analysis of expressed small RNAs in bacterial transcriptomes.
• Antisense RNA analysis: Detection and characterization of long antisense RNAs overlapping annotated genes.
• UTR profiling: Identification and quantification of 5' and 3' untranslated regions (UTRs) of mRNAs.
• Genome annotation improvement: Augmentation of genome annotations by adding expressed intergenic features.
• Transcriptomic quantification and DE: Measurement of transcript abundance and differential expression to study regulatory mechanisms and responses to environmental changes.

Methodology:

Coverage-based detection of expressed regions from RNA-seq reads mapped to a reference genome, followed by prediction and annotation of intergenic expressed regions, expression-strength filtering, transcript abundance quantification, and differential gene expression testing.