Figure 1

The construction of exons and isoforms from the alignment result of TopHat. (a) 9 exons are constructed from the alignment result of TopHat where the dotted line means a junction detected by a read and one arrow line represents a detected junction between two exons; (b) four possible isoforms constructed from source exon 1 to sink exon 9 using path finding algorithms from graph theory where l, x and ϕ indicate the exon length, the number of reads falling on this exon and the unknown abundance of each isoform, respectively.