structure of the transcript is hard to predict, as was investigated in the RNA-seq Genome Annotation Assessment Project (RGASP) (J Harrow, T Steijger, F Kokocinski, JF Abril, C Howald, A Reymond, A Mortazavi, B Wold, T Gingeras, R Guigó, et al., in prep.). We therefore look forward to “third-generation” sequencing methods such as Pacific Biosciences (Schadt et al. 2010) that show promise of generating longer reads of 1–2k, which will enable improvements in transcriptome annotation, facilitating the investigation of expression of each transcript structure within a cell during its development.
