Fig. 3
From: ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Novel gap-factors. The relationship among novel gap-factors, introns, and AS events is shown. Each subfigure depicts an example of novel gap-factor \(\left (p^{\prime }_{i},r^{\prime }_{i}\right)\) (gray boxes) in relation to a simple graph \(\mathcal {S}_{G}^{\star }\), where dashed arrows represent novel edges (not present in the splicing graph \(\mathcal {S}_{G}\)) and a read R. The two consecutive factors (pi,ri) and (pi+1,ri+1) of a spliced graph-alignment are represented by blue boxes, and the red lines represent the novel introns supported by the gap-factors. In terms of novel AS events, gap-factor (ε,ε) in case a supports an exon skipping, gap-factor \(\left (p^{\prime }_{i}, \epsilon \right)\) supports an intron retention in case b and alternative splice sites shortening an exon in case c. Finally, gap-factor \(\left (\epsilon, r^{\prime }_{i}\right)\) supports alternative splice sites extending an exon in case d and a new exon in case e