Sashimi Plot

Sashimi plots are quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the SAM/BAM format) and gene model annotations. Sashimi plots can be used to quickly screen di fferentially spliced exons along genomic regions of interest. 

To view a Sashimi plot of your alignment data, right click on the alignment track to bring up the pop-up menu, and select "Sashimi Plot".

If there is more than one feature track loaded, you will be presented with a dialog for choosing which track represents the gene annotations. Only one track can serve as feature annotations. If there is only one possible feature track (such as the reference genome gene track), this dialog is skipped. IGV will also prompt you to select which alignment tracks you would like to view in the Sashimi plot window. Any number of these can be selected. 

Once the input tracks are chosen, the Sashimi plot is displayed in a separate window (see examples below). The coverage for each alignment track is plotted as a bar graph. Arcs representing splice junctions connect exons. The thickness of each arc corresponds to the junction depth, which is displayed as a number in the arc. The gene annotation track is shown below the junction tracks. To view only those junctions which overlap a particular exon, select that exon by clicking on it. Multiple exons can be selected using ctrl + <click>. Clicking somewhere on the gene track, other than an exon, de-selects all exons.

You can zoom and pan this window in the same manner as IGV, however the boundaries are limited in size to the region IGV was viewing when the window was generated. It is recommended that the user set the view to the gene (or region) of interest before creating the plot. The current genomic coordinates are displayed just above the gene annotation tracks.

Static images of Sashimi plots can also be generated outside IGV with sashimi_plot, a Python tool which is part of the MISO package. Read more about sashimi_plot here.


Load example data from this session, or follow the steps below:

  • Start IGV, and load the genome Human hg18
  • Select File > Load from Server
  • Select BodyMap 2.0 > Merged 50bp and 75bp > Reads > Heart, Liver, and Kidney.
  • View gene SLC25A3 by entering it in the search bar.

Right-click on any alignment track and select "Sashimi Plot"

Check all 3 checkboxes, and click OK.

There are 3 isoforms for SLC25A3. Click on the 3rd exon of the top isoform (ID NM_005888), and you will see there are splice junctions only present in heart cells.

After selecting exon 3 for the top isoform, you will see this: