eXpress

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README : EXPRESS

eXpress is a streaming DNA/RNA sequence quantification tool. It has initially been tested for RNA-Seq transcriptome quantification but can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.

More details, installation instructions, and the manual can be found at http://bio.math.berkeley.edu/eXpress/

I. Authors:

The methods and algorithms used in eXpress were developed by Adam Roberts and Lior Pachter. Adam Roberts designed and wrote eXpress.

II. Requirements:

eXpress is a standalone tool that requires gcc 4.0 or greater, and runs on Linux Macintosh OS X, and Windows.

It depends on Boost (http://www.boost.org), BamTools (https://github.com/pezmaster31/bamtools), ZLIB (http://zlib.net/), and the Microsoft Visual C++ Runtime Library (Windows only) (http://www.microsoft.com/download/en/details.aspx?id=5555).

III. Learn More (Installation, Manual, etc.):

Installation steps, tutorial, manual, documentation, etc. are all available through the eXpress website: http://bio.math.berkeley.edu/eXpress/

Join the user group and mailing list to stay informed of updates and announcements: http://groups.google.com/group/express-users

IV. License:

eXpress is distributed under the Artistic License 2.0. Copyright (c) 2011-2013 Adam Roberts and Lior Pachter.

See included file LICENSE for details.

V. Acknowledgements:

• Cole Trapnell, primary developer of Cufflinks
• Derek Barnett, author of the BamTools API

VI. References:

Roberts A (2013). Thesis: Ambiguous fragment assignment for high-throughput sequencing experiments. EECS Department, University of California, Berkeley.

Roberts A and Pachter L (2012). Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods.

eXpress builds upon many ideas, including some proposed in the following papers:

Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B and Pachter L (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology.

Cappé O and Moulines E (2009). On-line expectation–maximization algorithm for latent data models. Journal of the Royal Statistical Society.

Pachter, L (2011). Models for transcript quantification from RNA-Seq. arXiv:1104.3889v2.

Roberts A, Trapnell C, Donaghey J, Rinn JL and Pachter L (2011). Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology.

Li B and Dewey C (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics.

VII. CONTACT:

Please send all questions, comments, and suggestions to [email protected].