title: Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.
abstract: 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, we go through the main steps of data processing and discuss open challenges and possible solutions.
authors.forename: Francesca
authors.initials: F
authors.lastname: Finotello
authors.forename: Barbara
authors.initials: B
authors.lastname: Di Camillo
mesh_terms: D000465:Algorithms; D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D012015:Reference Standards; D017423:Sequence Analysis, RNA / Q000379:methods*; D013223:Statistics as Topic
keywords: NGS; RNA-seq; differential gene expression; next-generation sequencing; transcriptomics