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 DESeq R package to calculate p-values from a negative binomial distribution for differential enrichment/ reduction. See Anders S, Huber W: Differential expression analysis for sequence count data. Nature Precedings. 2010 Jan

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

Documentation:

Misc:

Common mistakes:

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.

SourceForge.net Logo