We provide a novel web service, called rQuant.web, allowing convenient access to tools for quantitative analysis of RNA sequencing data. The underlying quantitation technique rQuant is based on quadratic programming and incorporates different biases induced by library preparation, sequencing, and read mapping. It can tackle multiple transcripts per gene locus and is therefore particularly well-suited to quantify alternative transcripts. rQuant.web is available as a tool in a Galaxy installation available at http://galaxy.fml.mpg.de. Using rQuant.web is free of charge, open to all users, and there is no login requirement.

The web service can be found here: http://galaxy.fml.mpg.de. rQuant.web is the web interface to the RNA-Seq quantitation tool rQuant that is described in [1], [2] and here.

Main Features

• Accurately predicts abundances of a given set of transcripts.
• Tackles mulitple transcripts per gene locus.
• Estimates biases induced by experimental settings.

Getting Started

An example how to use rQuant.web with an easy step-by-step explanation can be found here.

Workflow

Contact

In case of comments, problems, questions etc. feel free to contact

• Gunnar Rätsch
• Regina Bohnert

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.