CCB » Software » EDGE-pro

About 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.  

Obtaining the Software

This software is OSI Certified Open Source Software.   
Click to download the EDGE-pro software (v1.3.1) (Released 05/31/2013, current size is over 500MB)
To extract the files to the current directory type
     tar -vxf EDGE_pro_v1.3.1.tar.gz
The software was developed and tested on a Linux x86_64 system. Instructions for other platforms are provided in the MANUAL .


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Please reference our paper:
T. Magoc, D. Wood, and S.L. Salzberg. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. Evolutionary Bioinformatics vol.9, pp.127-136, 2013.  


This work is supported in part by NIH grants R01-LM006845-S, R01-HG006677, and R01-HG006102 to S.L. Salzberg.