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<h3>Data analysis</h3>
<p>The exploratory analysis, whose steps are shown in Figure <a href="http://nar.oxfordjournals.org/content/early/2016/05/27/nar.gkw486.full#F1" id="xref-fig-1-1">1</a>, was carried out with the ‘tuxedo’ software suite (Trapnell <em>et al</em>., 2010) and led to the definition of the Observed Transcriptome (ObsT). The conservative analysis (Figure <a href="http://nar.oxfordjournals.org/content/early/2016/05/27/nar.gkw486.full#F1" id="xref-fig-1-2">1</a>) was carried out by running the RNA-Seq by Expectation-Maximization (RSEM) package (Li & Dewey, 2011) and led to the definition of the RefT.</p>
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