A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhl?n M, Nielsen J. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 2012 Nov 01; 40(20):10084-97.