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soda examples



The source code for this example can be found on GitHub.

RepeatMasker-SODA was developed to visualize transposable elements (TE) as annotated by RepeatMasker. The example application is largely a reimplementation of the UCSC Genome Browser RepeatMasker Viz track with improved functionality.

Each annotation is displayed with the following parameters:

  • TE annotations are represented as rectangles
  • The outline color of the rectangles indicate the class of TE
  • The chevron pattern inside the rectangles indicates the chromosome strand on which the feature was located
  • The rectangles are internally shaded to indicate the inferred age of the feature, with lighter indicating older features
  • When rectangles are joined by angled lines, it indicates that we infer that the represented TE annotations collectively represent one feature in the genome
  • The horizontal dashed lines are projections of the portions of the TE sequence models that were not reported by RepeatMasker

  • For a more detailed description of these parameters, see the RepeatMasker Viz track settings page.