Identification of alternative isoforms using dRNA-seq. (A) Alternative splicing (AS) isoform classes. We built a transcriptome using the dRNA reads with StringTie2. We identified 332 alternative isoforms in 263 different genes. The plot shows one example of each of the four main classes of alternative isoforms detected. Diagrams of the exons of the reference and the alternative isoform as shown, together with the dRNA coverage along the gene. (B) Number of different types of splicing isoforms. Intron retention (IR) represents ∼80% of the events. (C) Number of isoforms per gene. In most cases, only one alternative isoform was detected. The most extreme case corresponds to wtf19, with two annotated isoforms and nine additional alternative isoforms detected here. (D) Relative abundance of reference and alternative isoforms for each gene. Data are for the genes containing at least one alternative isoform. The abundance is computed using the number of mapped dRNA reads; the fraction is then calculated over all isoforms containing mapped reads. Number of reference isoforms is 263 (two for wtf19); number of new alternative isoforms detected here, 332; median fraction reference isoforms, 0.873; and median fraction alternative isoforms, 0.105. (E) Abundance of reference and alternative isoforms. Number of dRNA reads mapped to reference and alternative isoforms. Numbers of isoforms as in D. (F) Skipped exons tend to be smaller than the complete set of exons in the reference annotations. Median length reference exons is 170; median length skipped exons, 63. P-value = 0.00752 Wilcoxon test.
