RNA-eXpress protocols

RNA-eXpress specifications


Unique identifier OMICS_01285
Name RNA-eXpress
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format BAM
Output data Some files including annotation, comparison statistics, sequence extraction and features counts.
Output format GTF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.4
Stability Stable
Registration required Yes
Maintained Yes


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  • person_outline Paul J. Hertzog <>

Publication for RNA-eXpress

RNA-eXpress IN pipeline

PMCID: 5846625
PMID: 28658212
DOI: 10.1038/nature22990

[…] kapa library quantification kit (kapa biosystems®). libraries were sequenced on an illumina miseq platform with the miseq reagent kit v3 or on a hiseq 2500. sequence reads were analyzed with the rna express application (illumina, basespace) or custom pipelines. alignment of reads to viral genomes was performed using bowtie and subsequently visualized using the integrative genomics viewer32 […]

RNA-eXpress institution(s)
Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, VIC, Australia
RNA-eXpress funding source(s)
Supported by the National Health and Medical Research Council, the ARC Centre of Excellence in Structural and Functional MIcrobial Genomics and the Victorian Government’s Operational Infrastructure Support Program.

RNA-eXpress review

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RNA-express is a great downloadable tool for handling RNA-sequencing data, annotating novel transcript features with ease