Sashimi

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the alignments plugin. View source.

The alignments display's sashimi setting: the junction arcs, over the coverage band or in a strip below it, and in that strip alone while coverage.show is off. The band counts each splice junction from the reads' N gaps and each same-reference join of a split read's segments by its class (junction.class: deletion, duplication, which a circRNA back-splice is, or inversion), once per pair of read-adjacent segments as the read arcs count support. A split junction always takes its class's read-arc color. Which junctions draw is the display's filter, by its junction fields.

Example usage#

{
  type: 'LinearAlignmentsDisplay',
  sashimi: { placement: 'auto', labels: { show: true } },
  filter: [
    { field: 'junction.reads', gte: 5 },
    { field: 'junction.canonical', equal: true },
    { field: 'junction.class', oneOf: ['splice', 'duplication'] },
  ],
}

Config slots#

A setting written to it names members one by one: a member left out stays as it is, and null resets one. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.