Figure 1. Estimation of significant changes in the abundance of variants. Mapped reads from RNA‐seq experiments in two experimental condition (top and middle) are used to quantify the alternative inclusion of an exon (white square) between flanking constitutive exons (green squares). In the first condition (top), 9 reads support the inclusion, and 1 read the exclusion of the alternative exon, in the second condition (middle) 2 inclusion and 4 exclusion reads are observed. A Fisher exact test is used to assess the statistical significance of the change in abundances between both conditions (p‐value = 0.036).

Figure 2. Graphical user interface of the Flux Simulator. The simulation pipeline comprises different steps: selection of a reference transcriptome which will be sequenced; in silico gene expression; and library construction and simulation of the obtained sequencing reads. The histograms in the screenshot show prospective read distributions along transcripts, broken down by different transcript lengths and expression levels. A simulated Northern blot summarizes the length distribution of the obtained cDNA fragments.