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Stage 2 app

Results from the svAmplicon pipeline are mainly intended for examination and curation in the associated Shiny app.

Load the data package ending with mdi.package.zip into the svAmplicon R Shiny app. The best way to run the app server is by installing the MDI Desktop, which gives you several options for running the server on your local computer, on your HPC server, or on a public web server.

Please see the instructions in the running app for details. The general steps are to:

  • load your desired pipeline data package(s)
  • rename samples and assign them into experimental groups
  • explore indvidual SV calls, keeping and rejecting individual reads based on quality assessments
  • download final results tables

Additionally, the app provide a genome track browser for visualizing the distribution of junctions within amplicon spans.

Use the Save your Work link at the left to save a bookmark of your work that you can load into the app server to restore the page to the same state.