Fig. 5
From: ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Spliced graph-alignment. Example of a spliced graph-alignment of a read R to a splicing graph \(\mathcal {S}_{G}^{\star }\) (in \(\mathcal {S}_{G}^{\star }\), the dashed arrows represent the novel edges not present in \(\mathcal {S}_{G}\)). The read R has been factorized in four strings r1, r2, r3, and r4 matching to strings p1, p2, p3, and p4 of P, which is the concatenation of exon labels of path π=〈A,B,D〉. This yields to the spliced graph-alignment \(\left (\left \langle (p_{1},r_{1}), \left (p_{1}^{\prime }, r_{1}^{\prime }\right), (p_{2},r_{2})\right.\right.\), \(\left.\left.\left (p_{2}^{\prime }, r_{2}^{\prime }\right), (p_{3},r_{3}), \left (p_{3}^{\prime }, r_{3}^{\prime }\right), (p_{4},r_{4})\right \rangle, \pi \right)\). We observe that \(p^{\prime }_{3}\), \(r^{\prime }_{1}\), \(r^{\prime }_{2}\), and \(r^{\prime }_{3}\) are equal to ε. Moreover, we note that \(\left (p_{1}^{\prime }, r_{1}^{\prime }\right)\), \(\left (p_{2}^{\prime },r_{2}^{\prime }\right)\) are two novel gap-factors, r2 matches p2 with an error of substitution while r4 matches p4 with an error of insertion: both the error and the cost of this spliced-graph alignment are equal to 2. This alignment of R to the splicing graph of G supports the evidence of two novel alternative splicing events: an alternative donor site of exon A and an intron retention on exon B