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Multi-quantitative tracks

TL;DR: a MultiQuantitativeTrack overlays many BigWig/bedGraph signals in one display. Use the bigWigs array for quick absolute-URL setups, or subadapters when you need relative URLs or per-subtrack color, group, and source.

MultiQuantitativeTrack config

Example MultiQuantitativeTrack config:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi",
  "name": "MultiWig",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "bigWigs": [
      "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
      "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
      "https://www.encodeproject.org/files/ENCFF858LIM/@@download/ENCFF858LIM.bigWig",
      "https://www.encodeproject.org/files/ENCFF425TNW/@@download/ENCFF425TNW.bigWig"
    ]
  }
}
Gotcha

The bigWigs shorthand only accepts absolute URLs; a relative path there will not resolve against the config's location. Use the subadapters form for relative URLs, which is also what you need for per-subtrack color, group, and source.

The source field

Each subtrack has a source identifier used as its label in the UI and carried on features as feature.get('source'). When using bigWigs, source is auto-derived from the URL filename. When using subadapters, set it explicitly. name is an alias, and source takes priority if both are set.

Since features carry a source attribute, you can reference it in jexl color callbacks, e.g. jexl:feature.source=='k1'?'red':'blue'.

The subadapters slot also supports:

  • color - default subtrack color
  • group - grouping label for organizing subtracks

Example:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "microarray_multi_groups",
  "name": "MultiWig (groups)",
  "category": ["ENCODE bigWigs"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "source": "k1",
        "color": "red",
        "uri": "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
        "group": "group1"
      },
      {
        "type": "BigWigAdapter",
        "source": "k2",
        "color": "blue",
        "uri": "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
        "group": "group2"
      }
    ]
  }
}

See the MultiWiggleAdapter config docs for all options.

Generating the subadapters from a samplesheet

Because subadapters is just an array of objects, it templates cleanly from repetitive data like an RNA-seq timecourse. Given rows of { timepoint, bigwig }, build the track in a script:

// rows: [{ timepoint: '0h', bigwig: 's3://.../t0.bw' }, ...]
const track = {
  type: 'MultiQuantitativeTrack',
  trackId: 'rnaseq-timecourse', // keep this stable across rebuilds
  name: 'RNA-seq timecourse',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MultiWiggleAdapter',
    subadapters: rows.map(row => ({
      type: 'BigWigAdapter',
      source: row.timepoint,
      uri: row.bigwig,
    })),
  },
}

See Deploying JBrowse Web for the full pattern of generating config.json from a samplesheet in a CI/CD pipeline.

Loading bedMethyl as a multi-quantitative track

modkit pileup produces a bedMethyl file, a tab-separated BED format where each row reports the methylation fraction at a single CpG position for one modification type (e.g. 5mC or 5hmC). It loads as BedTabixAdapter and maps to MultiQuantitativeTrack, with one subtrack per modification type:

modkit pileup sample.bam output.bedmethyl --ref reference.fa --preset traditional
bgzip output.bedmethyl
tabix -p bed output.bedmethyl.gz

--preset traditional produces 5mC calls (5hmC is combined into the 5mC fraction). Omit it for separate 5mC and 5hmC rows.

{
  "type": "MultiQuantitativeTrack",
  "trackId": "sample_modkit",
  "name": "CpG methylation (modkit)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/sample_modkit.bedmethyl.gz"
  }
}
jbrowse add-track-json '{
  "type": "MultiQuantitativeTrack",
  "trackId": "sample_modkit",
  "name": "CpG methylation (modkit)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://yourhost/sample_modkit.bedmethyl.gz"
  }
}'

JBrowse reads two of the columns:

  • score (column 11) — the percent methylation, 0–100
  • name (column 4) — the modification code, such as m for 5mC or h for 5hmC, used as the subtrack source label

In the "Add a track" form, pasting the URL to a .bedmethyl.gz file auto-detects BedTabixAdapter and MultiQuantitativeTrack.

See also