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 estimates 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 at http://galaxy.fml.mpg.de.