edge-pro
EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results. EDGE-pro includes routines to assign reads aligning to overlapping gene regions accurately. 15% or more of bacterial genes overlap other genes, making this a significant problem for bacterial RNA-seq, one that is generally ignored by programs designed for eukaryotic RNA-seq experiments.