Fig. 2

Hook hits orientations and coi filter. Estimation of the concordance orientation index (coi). Hooks potentially representing SLs are classified according to the orientation of their hits on the assembled transcripts with valid and invalid configurations. If SLFinder assumptions are met, the Hook hits should be primarily oriented in one of two valid configurations that depend on the orientation of the assembled transcript (red arrow for sense and blue for anti-sense) and the orientation of the generated Hooks. Note that Hooks could also be assembled in sense (black arrow) or anti-sense (grey arrow). a Valid Hook hits orientation and locations. b Invalid Hook hits orientation and locations. c Coi formula