USeq
Disclaimer:
This software is distributed with no warrantee or guarantee of fitness. See the open source BSD License.
What is USeq?
USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.
Initial emphasis: chIP-seq and RNA-Seq with FDR estimations. USeq is under continuous development at the
Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.
A description of the statistics and comparison of methods used in USeq is now published, see Nix DA, Courdy SJ, Boucher KM: Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks. BMC Bioinformatics. 2008 Dec 5;9(1):523.
Note, USeq now makes use of the DESeq2 R package to calculate p-values from a negative binomial distribution for differential enrichment/ reduction. See Love MI, Huber W, and Anders S (2014)
Read about USeq's 1st and 2nd place awards in the ChIP-Seq Community Challenge! PowerPoint Presentation , SEQanswers Forum
How to use/ install USeq?
To use USeq, download the latest release, install Java 1.6+, R, Storey's Q-Value and Anders' DESeq R libraries and launch the java jar applications with the -jar option.
For example, to execute 'ScanSeqs' type 'java -jar yourPathTo/USeq/Apps/ScanSeqs' on the command line to print a menu and description of options.
Afraid of the command line interface? No problem, give the GUI_ClickMe.jar a try. Launch it on Mac's and Windows by double clicking the application. This runs a draggable/ point and click wrapper
around the USeq applications.
Read the Usage guide. It contains detailed step-by-step instructions in how to use USeq applications to process your RNA-Seq and ChIP-Seq datasets.
Join the USeq Users mailing list to stay up to date with the latest USeq developments, tips, and tricks for next generation genomic analysis.
Requirements
- MacOSX or Linux, USeq apps are untested on Windows
- Java 1.6+
- R with Storey's Q-Value and Loves' DESeq2 libraries.
- Familiarity with command line programing
Documentation:
- Usage - Contains detailed tutorials in how to use USeq to process your sequencing data (ChIP-Seq, RNA-Seq, Bis-Seq etc).
- Applications - A listing of the various USeq applications.
- Menus - Command line menus/ instructions/ parameters for each of the applications.
- Release Notes - Changes associated with each release.
- Output File Type Descriptions - Description of the different types of file output generated by USeq applications.
- USeq Binary Archive Format - Description of the USeq Binary Archive format for storing and distributing massive genomic datasets.
- Developers Guide - Guide for java developers to create a USeq Eclipse project linked to the Sourceforge SVN.
- BSD License - The BSD open source USeq license.
Misc:
Common mistakes:
- No java sourced or installed. Type 'java -version' on the command line. It should be 1.6+
- Not using the -jar option. Type: 'java -jar -Xmx2G yourPathTo/USeq/Apps/ScanSeqs'
- Out of memory error. Increase the heap size with the -Xmx flag. Type: 'java -jar -Xmx3G yourPathTo/USeq/Apps/ScanSeqs'
- Trying to run the apps on Windows. It is worth a try. These have been tested on Linux and Mac OSX.
Questions? Comments? Post messages to the USeq Users Email List or, if needed, contact David Nix directly in the Bioinformatics Core.
Many thanks to Ken Boucher in the Biostatistics Shared Resource for help with the statistical methods.
Want to contribute? Join the USeq Users mailing list to stay up to date with the latest USeq developments, tips, and tricks for next generation genomic analysis.
