rQuant: Quantitative Detection of Alternative Transcripts with RNA-Seq Data

Software

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.

Talks/Conferences

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.

References

[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.