betAS pipeline enables intuitive visualization of AS changes. (A,B) Beta distributions (vertical “jitter” and density plots of the emitted values) illustrating PSI dispersion for each sample (A) and per phenotypic group (B), with the vertical dashed lines indicating the median PSI for each group, PSIneurons (dark red) and PSIESC (green). (C,D) Volcano plots illustrating the effect size (ΔPSI) as the difference between the median group PSIs and their significance assessed by the estimated probability of differential AS, based on the proportion of differences between ESC and neurons beta distribution randomly emitted values that are >0 (Pdiff) (C), and by the false positive rate (FPR) (D). Events are colored by the F-statistic, that is, the ratio of between- to within-group PSI variations (see Materials and Methods). Both y-axis scales are log-transformed to facilitate visualization. Upper row of trimmed points represents Pdiff > 0.9995 and FPR < 0.0001. (E–H) Beta distributions (density plots of the emitted values) and vast-tools’ PSIs (bottom, colored ticks) for selected events illustrative of different combinations of effect size and significance of AS differences, identified by vast-tools’ IDs (VAST-DB annotation for the mouse mm10 genome assembly): (E) MmuEX0003638 (gene Actn4, chr7:28895121–28895180), (F) MmuEX0001385 (gene 4833439L19Rik, chr13:54564515–54564621), (G) MmuEX0012381 (gene Commd6, chr14:101640288–101640299), and (H) MmuINT0085965 (gene Kctd17, chr15:78436995–78438486). (ESCs) Embryonic stem cells.
