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GCContentAdapter

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

Example usage

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

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

Computes GC content (or GC skew) from an assembly's sequence at render time, so there is no data file to prepare, and nothing to configure: the sequence comes from the assembly the track is displayed against.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "GCContentAdapter", ... }. 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.

SlotDescription
sequenceAdapter
frozen = null		don't set this — JBrowse computes GC from the assembly the track is displayed against. It stays as an escape hatch for scoring some other sequence, and setting it pins the track to that source even when the assembly's own sequence changes
advanced
windowSize
number = 100		width in bp of the window each score is computed over, centered on the position. 1 scores single bases; wider windows smooth the signal
advanced
windowDelta
number = 100		step in bp between successive windows. Equal to windowSize (the default) the windows tile without overlapping; smaller values overlap them, giving a denser, smoother signal for proportionally more work
advanced
gcMode
stringEnum (content, skew) = 'content'		calculate GC content fraction or GC skew (G-C)/(G+C)