Xpression is a RNA-seq analysis pipeline that uses free and open technologies to create gene expression profiles, mapping statistics and visualization files from next-gen sequencing data in a fast, flexible manner. Xpression is designed to be an easy-to-use, integrated solution for processing next-gen sequencing data derived from various types of samples, such as samples mapped to draft genomes and multiplexed samples.
Automated steps include quality filtering for sequencing and mapping, and gene expression profiling and normalization. It is especially well suited for analysis of bacterial sequence data.
Xpression can be run from command-line or from a GUI. The GUI is relatively intuitive and simple, allowing the running and queuing of multiple samples quickly and easily.
Once supporting software is installed, all you will need to start using Xpression is the Xpression GUI.
You can follow the Quick Start Guide using the Xpression example dataset or browse the the Documentation for more detailed implementation information.
Xpression requires a UNIX-like environment, such as Linux or MacOSX and recent versions of:
See Installation for details.
An environment configured for running Xpression is provided for those who do not have access to a Linux system or the capacity to install the needed software. Xpression VE is a graphical virtual environment that can be run in free software such as Oracle’s VirtualBox using all point-and-click control.
See Xpression Virtual Environment for details.
Please cite the following when you use our software:
Phattarasukol S, Radey M, Lappala C, Oda Y, Hirakawa H, Brittnacher M, and Harwood CS. 2012. Identification of a p-coumarate degradation regulon in Rhoodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing. Appl. Environ. Microbiol. In press.