EDGE-pro, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels 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.
Input files with gene coordinates in PTT and RNT format can be retrieved with the Get EDGE-pro Files tool available in Galaxy, or downloaded from the NCBI ftp repository. EDGE-pro accepts files in Sanger FASTQ format (Galaxy type fastqsanger). Use the FASTQ Groomer to prepare your files.
All 3 types of files (FASTA reference genome, PTT and RNT) must have the same order of chromosomes/plasmids (e.g. if chr1 is before chr2 in genome.fasta file, then chr1 must be before chr2 in ptt and rnt files as well). If there is no PTT or RNT file for one of chromosomes/plasmids, place this chromosome/plasmid at the end of the file.