Comparison of different pipelines based on their determined read counts that support each BSJ from the human fetal samples. Each point corresponds to one primer pair in one sample. Each panel (A–K) corresponds to a different pipeline by combining the three components from different methods. If the same method was used for multiple components, they are written together. For example, “B:psirc, FQf:Sailfish-cir” means the BSJs were identified by psirc, whereas both the full-length transcript isoforms and their expression levels were deduced by Sailfish-cir. All pipelines involving full-length quantification (Qf) aggregated the expression levels of all transcripts that involved a BSJ into the expression level of the junction.
