True positive isoforms in Set-up 1, annotation driven alignment and Mode 2 with IA. The panels depict the number of TP isoforms detected by methods in Mode 2 when IA is provided. They are divided in those that were already present in IA (bar in purple), and those not present in IA but retrieved by the methods. The latter are further divided in low, medium and high expression classes according to their true expression level. Panels A (upper left) refers to the case of 20M 100 bp-PE, Panels B (upper right) to 0.25M 100 bp-PE. Panels C (bottom left) and D (bottom right) are analogous to Panels A and B but for SE reads. All results are obtained with annotation driven alignment.
Angelini et al. BMC Bioinformatics 2014 15:135 doi:10.1186/1471-2105-15-135