Quantitative Transcriptome Analysis Using RNA-seq

RNA-seq has emerged as the technology of choice to quantify gene expression. This technology is a convenient accurate tool to quantify diurnal changes in gene expression, gene discovery, differential use of promoters, and splice variants for all genes expressed in a single tissue. Thus, RNA-seq experiments provide sequence information and absolute expression values about transcripts in addition to relative quantification available with microarrays or qRT-PCR. The depth of information by sequencing requires careful assessment of RNA intactness and DNA contamination. Although the RNA-seq is comparatively recent, a standard analysis framework has emerged with the packages of Bowtie2, TopHat, and Cufflinks. With rising popularity of RNA-seq tools have become manageable for researchers without much bioinformatical knowledge or programming skills. Here, the authors present a workflow for a RNA-seq experiment from experimental planning to biological data extraction.

Külahoglu C, Bräutigam A. (2014) Quantitative Transcriptome Analysis Using RNA-seq. Methods Mol Biol 1158, 71-91. [abstract]