Quantifying entire transcriptomes by aligned RNA-seq data

Abstract

Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and noncoding RNAs. Although RNA quality and library preparation protocols are the main source of variability, the bioinformatics pipelines for RNA-seq data analysis are very complex and the choice of different tools at each stage of the analysis can signifi cantly affect the overall results. In this chapter we describe the pipelines we use to detect miRNA and mRNA differential expression.