Sashimi Plot

Sashimi plots visualize splice junctions for multiple samples from their alignment data along side genomic coordinates and a user-specified annotation track. IGV displays the Sashimi plot in a separate window and allows for more manipulations of the plots than the junctions track

  1. To view a Sashimi plot of your alignment data, first zoom out the view to contain the entire region of interest as scrolling and zooming is limited to this initial region.
  2. Right click on a junctions track or alignment track to bring up the pop-up menu, and select Sashimi Plot.
  3. Select one features track to serve as the annotation.
    1. If there is only one possible feature track, i.e., the RefSeq genes track, then it is automatically loaded.
    2. If you loaded additional feature tracks, IGV presents a dialog for you to select a gene annotation track for the new plot.
  4. IGV prompts you to select which alignment tracks you would like to view as Sashimi plots. Select any number and press OK.

The Sashimi plot is displayed in a separate window. The coverage for each alignment track is plotted as a bar graph. Arcs representing splice junctions connect exons. Arcs display the number of reads split across the junction (junction depth). Genomic coordinates and the gene annotation track are shown below the junction tracks.

  • Hovering the mouse over each of the exons in the annotation displays additional information in a yellow tooltip.
  • Zoom in using the + button at top, and scroll by click-dragging the panel.
  • 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> and they will be highlighted as white boxes.
    • To clear selections, click on a blank area of the annotations section of the panel.

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.




Popup Menu Options

Command Description

Set Exon Coverage Max

  • Set the minimum and maximum data range for the track to display.
  • Option to log scale.
  • Data range is shown in brackets in the top left of each track.

Set Junction Coverage Min
Set Junction Coverage Max

  • Set minimum and maximum junction depth to include in display for each track.
Set Color
  • Adjust the color of the features for each track using multiple color options.
Show Exon Coverage Data
  • Selected by default.
  • Deselect to remove exon coverage data and data track range labels.
  • Text is default and displays the junction depth in text number for each arc.
  • Circle replaces the text with a circle amenable to labeling as shown in the Screenshot above.
  • None removes all labels.

Combine Strands
Forward Strand
Reverse Strand

  • Combine Strands is default and shows both + and – strand junctions.
  • Forward Strand displays only + strand junctions.
  • Reverse Strand displays only – strand junctions.

A junction's strandedness is determined by the BAM file XS tag value for the split read. How you assigned the XS tag values to the reads determines whether you potentially display novel junctions or display junctions reflecting previously determined junction annotations. See the Splice Junctions page for more details.

Save Image
  • Save the displayed image to your computer in .jpeg, .svg, .png, or .eps format.