To use outrigger, you must perform at least steps 1 and 3:

  1. outrigger index to read all your junctions in and create a database of alternatively spliced exons.
  2. outrigger validate to filter your splicing events for only those with valid introns. (optional)
  3. outrigger psi to calculate percent spliced in on your splicing events.


Each of these commands deserves its own page of explanation, so look at the links below.