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EDGE-Pro specifications

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Unique identifier OMICS_28042
Name EDGE-Pro
Alternative name Estimated Degree of Gene Expression in PROkaryotes
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Perl
Computer skills Advanced
Version 1.3.1
Stability Stable
Maintained Yes

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  • person_outline Edge-pro Team <>

Publication for Estimated Degree of Gene Expression in PROkaryotes

EDGE-Pro citations

 (12)
library_books

Gene Enrichment Analysis Reveals Major Regulators of Mycobacterium tuberculosis Gene Expression in Two Models of Antibiotic Tolerance

2018
PMCID: 5893760
PMID: 29670589
DOI: 10.3389/fmicb.2018.00610

[…] 2000., reads were de-multiplexed and adapter sequences removed to yield reads of 100-bp length. raw reads were mapped to the m. tuberculosis cdc1551 genome (genbank assembly gca_000669715.1) using edge-pro v1.3.1 (magoc et al., ) (running bowtie2 internally). samples containing fewer than 5 × 105 reads mapping to the cdc1551 genome were removed from the analysis (one sample) […]

library_books

Zinc Acquisition Mechanisms Differ between Environmental and Virulent Francisella Species

2018
PMCID: 5786701
PMID: 29109188
DOI: 10.1128/JB.00587-17

[…] with the illumina hiseq v4 platform., data analysis was performed by the uva bioinformatics core. briefly, gene reads were first aligned with reference genomes and read counts were quantified with edge-pro software. the deseq2 bioconductor package was then used to normalize the read counts and estimate dispersion for each gene. these data were then fitted to a negative binomial model, […]

library_books

Gene network analysis identifies a central post transcriptional regulator of cellular stress survival

2018
PMCID: 5869019
PMID: 29537368
DOI: 10.7554/eLife.33684.044

[…] the window identification number corresponds to the same sequence across the three different fasta sequences., mapping and quantification of reads to these windows was conducted using the edge-pro analysis pipeline (). a caveat of edge-pro quantification is the potential misattribution of reads to input windows. edge-pro quantification does not take strand information into account […]

library_books

Haem iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390

2017
PMCID: 5845736
PMID: 29171824
DOI: 10.1099/mic.0.000579

[…] total mrna was extracted, reverse transcribed and sequenced as described previously []. the sequence reads from each individual dataset were mapped to the s. aureus nctc 8325 genome using edge-pro [], and quantification of transcript abundance and calculation of differential gene expression were performed using deseq2 []. deseq2 uses the negative binomial distribution as a model […]

call_split

Endogenously generated 2 aminoacrylate inhibits motility in Salmonella enterica

2017
PMCID: 5636819
PMID: 29021529
DOI: 10.1038/s41598-017-13030-x
call_split See protocol

[…] erica subsp. enterica serovar typhimurium str. lt2 chromosome, complete genome (refseq accession number: nc_003197.1) and read counts were generated using the prokaryotic-tailored gene alignment tool edge-pro. genes differentially expressed (false discovery rate, fdr < 0.05) between the respective wild-type and rida strains of s. enterica were identified using deseq,,. briefly, an fdr < 0.05 […]

library_books

Transcriptomic responses of the olive fruit fly Bactrocera oleae and its symbiont Candidatus Erwinia dacicola to olive feeding

2017
PMCID: 5320501
PMID: 28225009
DOI: 10.1038/srep42633

[…] of genes relevant to the interaction of the fruit fly with its gut symbiont. the alignment of rna-seq reads to the draft transcriptome was performed with the bacterial-specific program edge-pro. using the reads per kilobase of transcript per million mapped reads (rpkm) as a ‘proxy’ of expression levels, we identified 81 over-expressed and the 41 under-expressed deges […]


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EDGE-Pro institution(s)
Center for computational Biology, McKusick-nathans institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
EDGE-Pro funding source(s)
Supported in part by the National Institutes of Health under grants R01-LM006845S, R01-HG006677, and R01-HG006102.

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