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. 2010 Jul;38(Web Server issue):W348-51.
doi: 10.1093/nar/gkq448. Epub 2010 Jun 15.

rQuant.web: a tool for RNA-Seq-based transcript quantitation

Regina Bohnert  1 , Gunnar Rätsch
Affiliations

rQuant.web: a tool for RNA-Seq-based transcript quantitation

Regina Bohnert et al. Nucleic Acids Res. 2010 Jul.

Abstract

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. Using rQuant.web is free of charge, it is open to all users, and there is no login requirement.

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Figures

Figure 1.
Figure 1.
Transcript profiles: (a) Normalized read coverage with respect to the relative transcript position is shown grouped by five different transcript length bins for the C. elegans SRX001872 data set (16); (b) The key component of rQuant is to infer the underlying read coverage of all transcripts at one gene locus (two transcripts in this illustration on the right: transcript 1 is shown in orange and transcript 2 in green), such that the differences between the observed (grey) and expected (blue) read coverage is minimized. The expected read coverage is inferred from the transcript abundances w1 and w2 and the transcript profiles (shown in the graphs on the right), which are inferred simultaneously for several loci.
See this image and copyright information in PMC

References

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