About EDGE-proEDGE-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 SoftwareThis 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 . |
Questions/Comments/RequestsSend an e-mail to edge.comments@gmail.com. |
ReferencesPlease reference our paper:T. Magoc, D. Wood, and S.L. Salzberg. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. |
FundingThis work is supported in part by NIH grants R01-LM006845-S, R01-HG006677, and R01-HG006102 to S.L. Salzberg. |
