Workflow of the stepwise selection in the AIDE method. Stage 1 starts with a single annotated isoform compatible with the most reads, and all the other annotated isoforms are considered as candidate isoforms. Stage 2 starts with the annotated isoforms selected in stage 1, and all the possible isoforms, including the unselected annotated isoforms, are considered as candidate isoforms. In the forward step in both stages, AIDE identifies the isoform that mostly increases the likelihood, and it uses the LRT to decide whether this increase is statistically significant. If significant, AIDE adds this isoform to its identified isoform set; otherwise, AIDE keeps its identified set and terminates the current stage. In the backward step in both stages, AIDE finds the isoform in its identified set such that the removal of this isoform decreases the likelihood the least, and it uses the LRT to decide whether this decrease is statistically significant. If not significant, AIDE removes this isoform from its identified set; otherwise, AIDE keeps the identified set. After the backward step, AIDE returns to the forward step. AIDE stops when the forward step in stage 2 no longer adds a candidate isoform to the identified set.
