Fusion transcript simulation. Example of fusion transcript simulation. (a) Original transcripts of three selected genes NPS, PR44, ATP5I. Boxes represent exons and solid lines refer to introns. (b) Illustration of three basic types of fusion transcripts. Hybrid fusions use exons from two distinct genes, Self fusions join exons from a single gene, Complex fusions use exons from three distinct genes. (c) Example of the available options for controlling fusion transcript generation. Split exons randomly selects breakpoints in the exons involved. Keep exon boundary forces fusion breakpoints to fall on exon boundaries. CDS only creates fusions using exons within the coding sequence region. Foreign insertion inserts a randomly generated sequence between fusion breakpoints. Auto-correct orientation forces FUSIM to correct the orientation of exons.