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rQuant: quantitative detection of alternative transcripts with RNA-Seq data

High-throughput sequencing technologies open exciting new approaches to transcriptome profiling. For the important task of inferring transcript abundances from RNA-Seq data, we developed a new technique, called rQuant, based on quadratic programming. Our method estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts.


The source code of rQuant is available at our FTP server. It also contains code for an installation in the Galaxy framework. Please also check out our web service rQuant.web. The source code is also available from the our git server.

Release History

Aug. 30, 2011 rQuant version 2.1 released. tar.bz2
Profiles can also be estimated empirically.
Option to use information from paired-end reads.
May 24, 2011 rQuant version 2.0 released. tar.bz2
New solver for optimisation problems.
Usage of commercial solver is no longer required.
May 18, 2011 rQuant version 1.2 released. tar.bz2
Transcripts from overlapping loci are jointly quantified.
Mar. 11, 2011 rQuant version 1.1 released. tar.bz2
Now also contains the tool ReadStats and some bug fixes.
Dec. 17, 2010 rQuant version 1.0 released. tar.bz2
First release of rQuant code.

Supplementary Data

The data that we used to evaluate rQuant, together with quantitation results can be downloaded from our FTP server.


Slides of the talk on "rQuant: Quantitative Detection of Alternative Transcripts with RNA-Seq Data" by Regina Bohnert at the Short-SIG of ISMB/ECCB 2009 in Stockholm, Sweden, on June 28, 2009 can be found here.


[1] Bohnert, R and Rätsch, G (2010): rQuant.web: a tool for RNA-Seq-based transcript quantitation, Nucleic Acids Research, 38(Suppl 2):W348-51.

[2] Bohnert, R, Behr, J, and Rätsch, G (2009): Transcript quantification with RNA-Seq data, BMC Bioinformatics, 10(S13):P5.

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