Figure 2.

Ability of the different methods to discover simulated isoforms. Simulation contains 2533 known isoforms (provided to the methods) and 1006 novel isoforms (811 exon skips, 195 intron retentions). (A) Overall precision and recall for discovering simulated isoforms (known + novel). (B) Recall for isoforms based on level of expression. (Hashed bars) Proportion of known isoforms; (solid bars) novel isoforms. While Cufflinks slightly outperforms iReckon on discovery of known isoforms with high abundance, the results on low-abundance isoforms are reversed, and iReckon outperforms the other methods at identification of all novel isoforms (size of solid sections of bars). (C) Precision and recall for discovery of novel isoforms, as well as recall specific to different types of alternative splicing simulated.