Harwood Lab - Xpression


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Xpression — An intergrated RNA-seq pipeline — Xpression 1.0rc1 documentation Navigation index modules \| next \| Xpression 1.0rc1 documentation » Xpression — An intergrated RNA-seq pipeline¶ Introduction¶ 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. Get started¶ Once supporting software is installed, all you will need to start using Xpression is the Xpression GUI. Follow the Xpression user guide or the Example dataset walkthrough for an introduction to analyzing RNA-seq data with Xpression. Browse the the code’s Documentation for more detailed implementation information or follow the Quick Start Guide for a more accelerated introduction. Xpression in action¶ Follow along with this video in the Example dataset walkthrough. Download¶ Depending on your system capabilites, Xpression is available in a number of forms. To obtain a file, first right-click, and then choose ‘Save As’ to save the file to your computer. Xpression GUI – UNIX-like systems, such as Linux. See Xpression user guide. Xpression VE – Complete Linux system configured to run Xpression GUI from any system. See Xpression Virtual Environment. Install Xpression – Automatic supporting-software installation script. See Installation. Xpression MacOS – Compatibility script needed to run Xpression GUI on MacOSX. You will also need the GUI itself, in the same directory as the script. Xpression AMI – Amazon machine image to be run on Amazon web services. See Amazon Web Services – the Cloud Xpression example dataset – sample CGA009 data, including genome, genbank and sequencing files. See Example Dataset. Requirements¶ Xpression requires a UNIX-like environment, such as Linux or MacOSX and recent versions of: Python 2 pysam biopython bwa samtools Java JRE See Installation for details. Alternatives¶ 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. We also have a Amazon virtual image that is configured to run the command-line version of Xpression. It is built on the standard Amazon linux image for safety and stability, and contains the latest version of Xpression, as well as supporting software. See Amazon Web Services – the Cloud. Feature requests and bug reporting¶ If there are features you think would improve Xpression or meet your research’s needs, or if there are issues or bugs that need to be resolved, please visit the code’s issue tracker. Bugs and feature requests can be more easily addressed there, as well as finding updates and news about Xpression. Publication¶ 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. Index¶ Quick Start Guide What you will need Procedure Download Xpression Example data Installation Requirements Install from package repository Install from source Alternatives Glossary: Xpression user guide Pipeline workflow overview Obtaining the Xpression GUI Starting Xpression Entering sample data and options Options window Storing parameters for later use Example dataset walkthrough Needed items Walkthrough video Start Xpression Entering Sample information Locating reference files Running Xpression Xpression Virtual Environment Installation of Xpression VE Increase resources Starting Xpression VE Example Dataset Reference genome fasta file Reference Genbank annotation file Sequence fastq file Documentation Pipeline overview Step 1 - Extract quality reads by barcode Step 2 - Map quality read to reference Step 3 - Count reads per locus Index Module Index Navigation index modules \| next \| Xpression 1.0rc1 documentation » © Copyright 2012, Harwood Lab, University of Washington. Last updated on 09:43 11 Jun, 2012. Created using Sphinx 1.1.3.