Comparison between AIDE and the other three isoform discovery methods in simulation. Given each synthetic annotation set, we applied AIDE, Cufflinks, StringTie, and SLIDE for isoform discovery and summarized the expression levels of the predicted isoforms using fragments per kilobase million reads mapped (FPKM) units. Then the precision-recall curves were obtained by thresholding the FPKM values of the predicted isoforms. The AUC of each method is also marked in the plot. The results shown are based on RNA-seq data with a 10 × coverage.