Xpression – an integrated RNA-seq analysis pipeline

Xpression automatically processes quality filtering, mapping, expression profiling, and visualization from short read-length NGS reads in nucleotide-space (e.g., Illumina). It currently uses BWA to map reads, which allows a specified number of mismatches between read and reference genome. The expression profile provides normalization for reads per million (pM) and per million-kilobase (pKM). It can also take read orientation of the reads into account if strand-specificity was maintained during the library-prep method.

This pipeline can be run on UNIX-like systems via the command-line or graphically via Java. To run Xpression on any system, such as Windows, a fully-configured virtualized environment is also provided. This environment needs software such as VirtualBox to run, which can be downloaded and installed with a standard point-and-click wizard interface.

The Integrative Genomics Viewer (Broad) is recommended for viewing the wiggle-format visualization files, and we have found Tablet to be a good choice for viewing the sorted bam files.

The project website:
The code’s home (including the issue tracker and source):

Additionally, the design of the tool allows flexible use and easy modification to suit specific needs.

  • Phattarasukol S, Radey M, Lappala C, Oda Y, Hirakawa H, Brittnacher M, and Harwood CS. (2012) Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing. Appl Environ Microbiol [Epub ahead of print]. [abstract]