EDGE-pro

EDGE-pro estimates gene expression from prokaryotic RNA-seq data to quantify transcription at the gene level in bacterial and archaeal genomes.

Key Features:

• Prokaryote-Specific Design: Optimized for gene-dense prokaryotic genomes to produce per-gene expression estimates for bacteria and archaea.
• Alignment Methodology: Uses Bowtie2 for non-spliced alignments and explicitly accounts for overlapping genes common in bacterial genomes.
• Pipeline Structure: Implemented as a pipeline of C++ and Perl programs that process RNA-seq data to generate gene expression estimates.

Scientific Applications:

• Expression Measurement: Provides greater sensitivity and accuracy for measuring gene expression compared to microarray-based methods.
• Gene Regulation Analysis: Enables investigation of bacterial gene regulation and function by delivering precise gene-level quantification.

Methodology:

Processes raw RNA-seq data using Bowtie2 for non-spliced alignments, handles overlapping genes, and executes as a C++ and Perl pipeline.