Genomics: the state of the art in RNA-seq analysis

We often talk about the genome as the ‘book of life’ for an organism. To appreciate the gene expression problem, we need a slightly different analogy. Let’s consider the transcriptome to be the ‘newsstand of life’ (Fig. 1). Some magazines (RNAs) have many copies on the shelf, whereas others are sold out. In the ‘old days’, newsagents would carry only the most popular magazines; each magazine was expensive, and so you only bought a few. Today (because of changes in sequencing methods and associated technologies), you buy the whole newsstand for one bargain price. The only catch is that the newsagent puts them all through a paper shredder first. Fortunately, in this imaginary world, there are armies of tape-wielding do-gooders (algorithm developers) eager to put your magazines back together and a statistics junkie (RGASP) who organizes a competition to find out who does the best job. The process of reassembling the magazines is called transcript reconstruction, and it is the main emphasis of the paper from Steijger et al.1. One of the underlying technologies in transcript reconstruction involves mapping RNA-seq reads back to the parent genome, which is the subject of the Engström et al. paper2.