CrisprGuideAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the sequence plugin. View source.

Example usage#

The defaults are SpCas9 — NGG PAM, 20 nt guide, 3' PAM — so a track needs no slots at all. It scans the assembly's own sequence, which is why there is no file location:

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'CrisprGuideAdapter',
  },
}

Example: a different nuclease#

Cas12a/Cpf1 reads a TTTV PAM at the 5' end with a longer guide, and cuts far from the PAM — so pamLocation and both cut offsets move too, or the guides are found in the right places and drawn cutting in the wrong ones:

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'CrisprGuideAdapter',
    pam: 'TTTV',
    pamLocation: '5prime',
    guideLength: 23,
    cutOffset: 18,
    cutOffsetBottom: 23,
  },
}

See the Config slots section below for all available configuration fields.

Note: don't set sequenceAdapter — JBrowse supplies it from the assembly the track is displayed against. Setting it by hand pins the scan to one sequence source and silently desyncs the track if the assembly's sequence changes.

Related links#

• Track: FeatureTrack
• Display: LinearArcDisplay
• Display: LinearBasicDisplay
• Display: LinearMultiRowFeatureDisplay
• Display: LinearScoreDisplay
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "CrisprGuideAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. 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.