The exploratory analysis, whose steps are shown in Figure 1, was carried out with the ‘tuxedo’ software suite (Trapnell et al., 2010) and led to the definition of the Observed Transcriptome (ObsT). The conservative analysis (Figure 1) was carried out by running the RNA-Seq by Expectation-Maximization (RSEM) package (Li & Dewey, 2011) and led to the definition of the RefT.