I have been struggling to find a good package to create and customize sashimi plots. For example, I would like to be able to remove intermediate genomic regions if I want to visualize large splice junctions. Let's say the junctions spans from gene A to gene D, then I would like to remove the 'noice' of the splicing of the genes that lay in between gene A and D. Additionally, I would like to use BAM files as input to visualize also the read count covering the junctions and compare healthy vs. tumor samples.
Since it is not possible to customize IGV to those needs and it comes an unclear figure upon large junctions, I am looking for packages that are able to create sashimi plots and customize those to my needs.
Suggestions are very welcome!