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. 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. Note: The track can also be computed dynamically from an Alignment track by enabling the "Show splice junctions track" option in the alignment preferences.
Junction files should be in the standard .bed format. The 'score' field is used to indicate depth of coverage.
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. All junctions with more than 50 reads have the same thickness. Hovering the mouse over a junction will display the coverage.