title: RNA-Seq: revelation of the messengers.
abstract: Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the technology of choice for whole-transcriptome studies. However, the bioinformatics skills required for RNA-Seq data analysis often pose a significant hurdle for many biologists. Here, we put forward the concepts and considerations that are critical for RNA-Seq data analysis and provide a generic tutorial with example data that outlines the whole pipeline from next-generation sequencing output to quantification of differential gene expression.
authors.affiliation: Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Marcel C
authors.initials: MC
authors.lastname: Van Verk
authors.forename: Richard
authors.initials: R
authors.lastname: Hickman
authors.forename: Corné M J
authors.initials: CM
authors.lastname: Pieterse
authors.forename: Saskia C M
authors.initials: SC
authors.lastname: Van Wees
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger