Sashimi-plot is a utility for automatically producing publication-quality plots for RNA-Seq analyses of isoform expression. It is part of the MISO framework. In particular, sashimi-plot can: (1) plot raw RNA-Seq densities along exons and junctions for multiple samples, while simultaneously visualizing the gene model/isoforms to which reads map, and (2) plot MISO output alongside the raw data or separately.
Katz Y, Wang ET, Airoldi EM, Burge CB. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 7, 1009-1015. [abstract]