RNA-Seq is rapidly becoming the standard technology for transcriptome analysis. Fundamental to many of the applications of RNA-Seq is the quantification problem, which is the accurate measurement of relative transcript abundances from the sequenced reads.
The authors review many recently published models that are used to estimate the relative abundances. In addition to describing the models and the different approaches to inference, they also explain how methods are related to each other. They also review the applications of RNA-Seq models to differential analysis, and explain why accurate relative transcript abundance estimates are crucial for downstream analyses.
They found that inference with many of the models results in identical estimates of relative abundances, even though model formulations can be very different. In fact, they show how a single general model captures many of the elements of previously published methods.
Pacter L. (2011) Models for Transcript Quantification from RNA-Seq. arXiv:1104.3889.[article]