I'm using Gviz to make read-coverage and Sashimi plots for a paper, and I'd like to extract information about how many reads contribute to each splice junction in the Sashimi plot. These numbers must be inferred at some point since Gviz is generating the AlignmentsTrack object directly from the BAM file, but it's not clear to me whether it's possible for a user to get access to the intermediate steps used to generate the Sashimi plot. Is there a way to do this?

Hi, You can simply read in the part of your BAM file with GAlignments function and afterwards extract junction counts with summarizeJunctions, both function come from GenomicAlignments package.