The heuristic junction projection module builds all the candidate Junction regions, taking into account the strand-mapping of each read pair to the corresponding chromosome and the physical strand occupancy of the associated genes. The Junction Projection depth (JPD) is user customizable (red box, default = 3), ranging from 0 (i.e. only the two exons deterministically found by the Junction Prediction Algorithm are considered) to the infinity (i.e. all the candidate exons pertaining the two genes). The JPD defines how deep the heuristic projection is. The deeper the projection, the higher the chance to heuristically identify a ‘hidden’ junction, at a price of longer processing times.