RNA-seq is a methodology for RNA profiling based on next-generation sequencing that enables to measure and compare gene expression patterns at unprecedented resolution. Although the appealing features of this technique have promoted its application to a wide panel of transcriptomics studies, the fast-evolving nature of experimental protocols and computational tools challenges the definition of a unified RNA-seq analysis pipeline. In this review, focused on the study of differential gene expression with RNA-seq, the authors outline the main steps of data processing and discuss open challenges and possible solutions.
Challenges and strategies for RNA-Seq data analysis
Finotello F, Di Camillo B. (2014) Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis. Brief Funct Genomics [Epub ahead of print]. [abstract]