Splice Junctions

IGV supplements each alignment track with (1) a coverage track and (2) if selected in the Alignment Preferences panel, a default splice junctions track.  This section pertains to the default junctions track as well as to independently loaded junctions data. For plots that can provide more detailed junction information, see Sashimi Plots.

  • By default the Show splice junctions track option is disabled in the Alignment Preferences panel.
    • When enabled, IGV dynamically computes a junctions track from alignment data.
  • Independent junctions files should be in the standard .bed format. 

Splice Junctions Track

Each splice junction is represented by an arc from the beginning to the end of the junction. 

  • Junctions from the + strand are colored red and extend upward from the center line. 
  • Junctions from the – strand are blue and extend downward.
  • The height of the arc, and its thickness, are proportional to the depth of read coverage.
    • However, all junctions with more than 50 reads have the same thickness (first image). 
    • Display a more proportionate representation by selecting Autoscale from the right-click menu (second image).

Hovering the mouse over a junction will display the coverage. The first screenshot shows multiple coverage detail panels for each three components of two splice junctions on opposite strands.

  • Read depth for each end of the junction is displayed. For the red junction below, starting flank depth is 109 reads and ending flank depth is at 6606 reads.
  • Other details for a given junction's three hover elements are the same.



Enable junctions view for .bed files

The splice junction view displays an alternative representation of .bed files encoding splice junctions, such as the "junctions.bed" file produced by the TopHat program. Display details are as described in the section above.

  • This view is enabled by including a track line that specifies either name=junctions or graphType=junctions.
  • TopHat's "junctions.bed" file includes a track line specifying name=junctions by default, so no action is required for these files.

The track can also be computed dynamically from an Alignment track by enabling the Show splice junctions track option in the alignment preferences as described above.

Junction files should be in the standard .bed format.  The score field is used to indicate depth of coverage.