As the name implies, RNA sequencing (RNA-seq) is a technique used to determine the nucleotide sequences of RNA molecules. By counting the number of these sequences we can measure how many different RNA molecules are in our original sample. With qPCR and microarrays, we need to decide which genes we want to measure before we run our experiments. RNA-seq is different because we can measure any RNA molecules present in our sample without any prior planning or knowledge. While RNA-seq offers many advantages over the older technologies, it is more expensive, and the analysis of RNA-seq data is much more complex.
Which technique would you use if you are trying to discover new genes: microarray or RNA-seq?