Sashimi Plot

Sashimi plots quantitatively 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. Use Sashimi plots to screen di fferentially spliced exons along genomic regions of interest. 

  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 view.
  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.

Example Sashimi plot

The screenshot above (2015.4.16) shows the Sashimi plot of the example data from the Splice Junctions page with the addition of kidney tissue data.

  • Load Human hg19 genome and from the server Body Map 2.0 > Alignments > Merged 50bp and 75bp > Heart, Kidney, and Liver. Type SLC25A3 in the search bar.
  • Right-click on the junctions or alignment track and select Sashmi plot from the menu. Select all three boxes to continue plotting the three tissues and click OK.
  • Filter out low-count splicing events by right-clicking on a track and selecting Set Junction Coverage Min. Enter 50 and click OK. Repeat for the other tracks.
  • For the given RefSeq gene annotation displayed at the bottom, there are three isoforms for SLC25A3. To see only the splice junctions that connect to a specific exon, in this example an exon used differentially by heart cells, click on the third exon of the middle isoform (white exon in Screenshot 2015.4.16). Return to viewing all junctions by clicking on an empty region of the annotations section.

  • Prepare a splice junction view for use in a presentation, e.g. the Screenshot example below (2015.4.17).
    • Zoom into and center the 5' end of the loci by clicking the + button and click-dragging the display to the right.
    • Right-click on the panel and select Circle to replace the junction numbers with circles.
    • Right-click on the panel and select Save Image to save as .jpeg, .svg, .png, or .eps.

Right-click pop-up menu options for Sashmi plots

These options were expanded with IGV v2.3.47, released March 2015.

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.