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Hi-C track

TL;DR: a HicTrack with a HicAdapter needs only the .hic file location. Loop and interaction calls (BEDPE) are a separate VariantTrack drawn with a LinearPairedArcDisplay.

{
  "type": "HicTrack",
  "trackId": "hic",
  "name": "Hi-C Track",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic"
  }
}
jbrowse add-track https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic \
  --trackId hic \
  --name "Hi-C Track" \
  --assemblyNames hg19

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "HicTrack",
  "trackId": "hic",
  "name": "Hi-C Track",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic"
  }
}

HicAdapter takes the .hic file through the uri shorthand; the longhand slot is hicLocation (HicAdapter).

Display settings

The coloring and its controls are LinearHicDisplay slots, and adjusting the color scale shows what each does to the picture:

{
  "type": "HicTrack",
  "trackId": "hic_kr",
  "name": "Hi-C (KR, log scale)",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic"
  },
  "displayDefaults": {
    "selectedNormalization": "KR",
    "useLogScale": true,
    "colorScheme": "viridis",
    "showLegend": true
  }
}
jbrowse add-track https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic \
  --trackId hic_kr \
  --name "Hi-C (KR, log scale)" \
  --assemblyNames hg19 \
  --displayDefaults '{"selectedNormalization":"KR","useLogScale":true,"colorScheme":"viridis","showLegend":true}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "HicTrack",
  "trackId": "hic_kr",
  "name": "Hi-C (KR, log scale)",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic"
  },
  "displayDefaults": {
    "selectedNormalization": "KR",
    "useLogScale": true,
    "colorScheme": "viridis",
    "showLegend": true
  }
}
  • selectedNormalization names the matrix-balancing scheme (KR, SCALE, VC, VC_SQRT, NONE). JBrowse resolves it against what the file provides, so a scheme the file lacks falls back with no error (normalization)
  • resolutionBias is a signed offset from the zoom-derived binsize, so the choice survives zooming: negative is finer, positive coarser

Loops and interactions as arcs

BEDPE loop calls load as a VariantTrack with a LinearPairedArcDisplay. color is evaluated per feature and lineWidth is the arc stroke in pixels. This draws only the high-scoring calls, in dark red, as thin arcs:

{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://example.com/loops.bedpe.gz"
  },
  "displays": [
    {
      "type": "LinearPairedArcDisplay",
      "color": "jexl:feature.score>=500?'#8b1a1a':'rgba(0,0,0,0)'",
      "lineWidth": 1
    }
  ]
}
jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://example.com/loops.bedpe.gz"
  },
  "displays": [
    {
      "type": "LinearPairedArcDisplay",
      "color": "jexl:feature.score>=500?'\''#8b1a1a'\'':'\''rgba(0,0,0,0)'\''",
      "lineWidth": 1
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://example.com/loops.bedpe.gz"
  },
  "displays": [
    {
      "type": "LinearPairedArcDisplay",
      "color": "jexl:feature.score>=500?'#8b1a1a':'rgba(0,0,0,0)'",
      "lineWidth": 1
    }
  ]
}

Compartments and subcompartments

The compartment eigenvector is a BigWig, drawn as a quantitative track in two colors around zero. Pin minScore and maxScore when two of these tracks are read against each other, so neither autoscales to its own extremes; the user guide covers the sign check that goes with it:

{
  "type": "QuantitativeTrack",
  "trackId": "hic_compartments",
  "name": "Compartment eigenvector",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig"
  },
  "displayDefaults": {
    "minScore": -0.03,
    "maxScore": 0.03
  }
}
jbrowse add-track https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig \
  --trackId hic_compartments \
  --name "Compartment eigenvector" \
  --assemblyNames hg38 \
  --displayDefaults '{"minScore":-0.03,"maxScore":0.03}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "QuantitativeTrack",
  "trackId": "hic_compartments",
  "name": "Compartment eigenvector",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig"
  },
  "displayDefaults": {
    "minScore": -0.03,
    "maxScore": 0.03
  }
}

Subcompartments are a BED whose color column carries the class color. ENCODE's copies are not tabix-indexed, so the plain BedAdapter reads the whole file:

{
  "type": "FeatureTrack",
  "trackId": "hic_subcompartments",
  "name": "Subcompartments",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2022/08/26/7165fc3e-f186-4fba-be87-f4ea600404b0/ENCFF247IAA.bed.gz",
    "columnNames": [
      "chrom",
      "chromStart",
      "chromEnd",
      "name",
      "score",
      "strand",
      "thickStart",
      "thickEnd",
      "itemRgb",
      "numAltClusterings",
      "altClusterNum",
      "altClusterAssignment"
    ]
  }
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "hic_subcompartments",
  "name": "Subcompartments",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2022/08/26/7165fc3e-f186-4fba-be87-f4ea600404b0/ENCFF247IAA.bed.gz",
    "columnNames": [
      "chrom",
      "chromStart",
      "chromEnd",
      "name",
      "score",
      "strand",
      "thickStart",
      "thickEnd",
      "itemRgb",
      "numAltClusterings",
      "altClusterNum",
      "altClusterAssignment"
    ]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "hic_subcompartments",
  "name": "Subcompartments",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2022/08/26/7165fc3e-f186-4fba-be87-f4ea600404b0/ENCFF247IAA.bed.gz",
    "columnNames": [
      "chrom",
      "chromStart",
      "chromEnd",
      "name",
      "score",
      "strand",
      "thickStart",
      "thickEnd",
      "itemRgb",
      "numAltClusterings",
      "altClusterNum",
      "altClusterAssignment"
    ]
  }
}

columnNames does two jobs here, and neither failure it prevents raises an error:

  • The file's last three columns are not BED12's block fields, so the positional layout takes the cluster count for a blockCount and grows every feature a row of nonexistent subfeatures
  • Naming column nine itemRgb is what paints the classes their own colors. The file's header spells it itemRGB, which JBrowse does not look for, and a second comment line follows the column line, so the parser takes that last line as the definition and finds no tab-separated fields in it

See also