Figure 2. Splice junction read coverage is correlated with unimodality of splicing distributions.

(a) Comparison of splice junction read coverage and observed $\widehat{\mathrm{\Psi }}$ for three cassette exons in the Chen dataset, with low (Cadm1 exon 8; chr9: 47829377–47829409), medium (Thyn1 exon 6, chr9: 27006801–27006951), and high coverage (Rbm39 exon 3; chr2: 156178880–156178952). Each dot represents the $\widehat{\mathrm{\Psi }}$ of that exon in one cell. (b) $\widehat{\mathrm{\Psi }}$ distribution of the 300 highest coverage cassette exons with intermediate splicing (average $\widehat{\mathrm{\Psi }}$ between 0.2 and 0.8) in each of the six analyzed datasets. Each row in the heatmap shows the distribution of $\widehat{\mathrm{\Psi }}$ for one exon across all cells. (c) Relationship between the average read coverage and proportion of binary observations for each cassette exon in the Chen dataset. (d) Correlation between the total number of splice junction reads captured in each cell, and proportion of cassette exons with intermediate splicing that show binary $\widehat{\mathrm{\Psi }}$ in that cell.

Figure 2—figure supplement 1. Junction read coverage determines the proportion of binary observations in all analyzed datasets.

(a) As in Figure 2c, the splice junction read coverage of an intermediate exon was anti-correlated with the proportion of cells in which it shows binary $\widehat{\mathrm{\Psi }}$ (only one isoform is observed) in all datasets. Barplot: Pearson correlation between read coverage and proportion of binary observations of each cassette exon. (b) As in Figure 2d, the total number of splice junction reads in a cell was inversely proportional to the fraction of exons that have binary values in the cell in all datasets. Barplot: Pearson correlation between the total number of captured reads in each cell and the proportion of cassette exons with binary $\widehat{\mathrm{\Psi }}$. (c) Relationship between transcriptional burst frequency and size, and the proportion of binary observations of an exon. (d) $R^2$ of the linear regression prediction of the proportion of binary observations per exon based on burst frequency, size, number of reads, and a combination of these features.