Gene-level isoform discovery and abundance estimation results of AIDE, Cufflinks, StringTie, and SLIDE on simulated RNA-seq data with 10 × coverage. Each box gives the first quantile, median, and third quantile of the gene-level accuracy given each of the nine sets of synthetic annotations. (A) Precision rates in isoform discovery; (B) recall rates in isoform discovery; and (C) error rates (defined as one-half of the sum of the absolute differences between the true and estimated isoform proportions) in abundance estimation.