Fig. 3

eCLIP data analysis with JACUSA2. a Schematic representation of the JACUSA2 principle. Fragments from eCLIP and SMinput datasets generated by Reverse transcription (RT) stop at different positions indicated on the top. As an example, the Stop Rate Difference (SRD) calculation is indicated for the position 4 (yellow dots). b Distribution of positions with Stop Rates that have a p-value < 0.05, plotted relative to the exon junction. The vertical gray line represents the position − 27, while the blue area that spans from − 23 to − 32, corresponds to the window used for calculating the SRD score per exon. c Stacked bar plot showing the count of detected exons and unloaded exons per exon group (first, internal, and last). d The bar plot illustrates the distribution of detected exons in different expression classes for exons from all genes, excluding the last exon. Each bar represents a bin of equal size, and the percentage of loaded exons out of the total is indicated on top of each bar. e Stacked bar plot correlating uridine count in the previously selected window with the relative percentage of exons corresponding to either detected or undetected categories. The numbers indicated in each bar represent the total number of exons (top) and the number of loaded exons (below)