Examples of CLASS predictions outperforming other programs' on the simulated single-end read data. (a) Cufflinks fails to predict a transcript at the DDX12P gene locus, whereas CLASS predicts the full transcript. (b) CLASS finds more of the splice forms, including alternative 5' and 3' terminal exons, for the C1S gene. (c) Cufflinks produces spurious isoforms, including a short single-exon transcript and a 5 bp variation on exon 22, for the DDX11 gene. The reference ENSEMBL transcripts sampled by the reads are shown in the top panels.