Hi-C track

A HicTrack with a HicAdapter needs only the .hic file location. Loop and interaction calls (BEDPE) are a separate VariantTrack drawn as link marks on a LinearMarkDisplay.

Config file

Goes in the tracks array of config.json. See Tracks.

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

CLI (add-track)

jbrowse add-track https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic \
  --trackId hic \
  --name "Hi-C Track" \
  --assemblyNames hg19

In the app

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

Main file: https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

Track name: Hi-C Track
Assembly: hg19

Click Add.

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:

Config file

Goes in the tracks array of config.json. See Tracks.

{
  "trackId": "hic_kr",
  "name": "Hi-C (KR, log scale)",
  "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic",
  "assemblyNames": ["hg19"],
  "displayDefaults": {
    "data": { "normalization": "KR" },
    "encoding": {
      "color": { "scale": { "type": "log", "scheme": "viridis" } }
    },
    "legend": { "show": true }
  }
}

CLI (add-track)

jbrowse add-track https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic \
  --trackId hic_kr \
  --name "Hi-C (KR, log scale)" \
  --assemblyNames hg19 \
  --displayDefaults '{"data":{"normalization":"KR"},"encoding":{"color":{"scale":{"type":"log","scheme":"viridis"}}},"legend":{"show":true}}'

In the app

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:

{
  "trackId": "hic_kr",
  "name": "Hi-C (KR, log scale)",
  "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic",
  "assemblyNames": ["hg19"],
  "displayDefaults": {
    "data": { "normalization": "KR" },
    "encoding": {
      "color": { "scale": { "type": "log", "scheme": "viridis" } }
    },
    "legend": { "show": true }
  }
}

data.normalization 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)
data.resolution is a signed offset from the zoom-derived binsize, so the choice survives zooming: positive is finer, negative coarser
encoding.color.scale.domainMax pins the count the color scale saturates at. Unset, it follows the loaded counts, so two tracks given the same number share one scale
encoding.color.field is observed, the counts, or observed/expected, each count over the file's expected count at its distance, drawn diverging around 1 (compartments)

Comparing two conditions

A controlAdapter on the adapter names a second .hic, and the observed/control field draws each count over the control's, both scaled to one library depth. This track is K562 over GM12878:

Config file

Goes in the tracks array of config.json. See Tracks.

{
  "type": "HicTrack",
  "trackId": "hic_k562_over_gm12878",
  "name": "K562 over GM12878",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/4d332729-3463-4782-b33c-76e4fa8ff72a/ENCFF080DPJ.hic",
    "controlAdapter": {
      "type": "HicAdapter",
      "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/6f0cc163-86c7-4a68-baac-65af90f5a90d/ENCFF053VBX.hic"
    }
  },
  "displayDefaults": { "encoding": { "color": "observed/control" } }
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "HicTrack",
  "trackId": "hic_k562_over_gm12878",
  "name": "K562 over GM12878",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/4d332729-3463-4782-b33c-76e4fa8ff72a/ENCFF080DPJ.hic",
    "controlAdapter": {
      "type": "HicAdapter",
      "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/6f0cc163-86c7-4a68-baac-65af90f5a90d/ENCFF053VBX.hic"
    }
  },
  "displayDefaults": { "encoding": { "color": "observed/control" } }
}'

In the app

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_k562_over_gm12878",
  "name": "K562 over GM12878",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "HicAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/4d332729-3463-4782-b33c-76e4fa8ff72a/ENCFF080DPJ.hic",
    "controlAdapter": {
      "type": "HicAdapter",
      "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/6f0cc163-86c7-4a68-baac-65af90f5a90d/ENCFF053VBX.hic"
    }
  },
  "displayDefaults": { "encoding": { "color": "observed/control" } }
}

The track menu's Compare with... builds the same track from two tracks already loaded (comparing two conditions).

Loops and interactions as arcs

BEDPE loop calls load as a VariantTrack with a mark display drawing one link per call: a mate step reads each record's other end, x2 names the fields holding it, strokeWidth is the stroke in pixels and color the stroke color. A filter step keeps the high-scoring calls, drawn here in dark red as thin arcs:

Config file

Goes in the tracks array of config.json. See Tracks.

{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "uri": "https://example.com/loops.bedpe.gz",
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "color": { "value": "#8b1a1a" }, "strokeWidth": 1 },
          "transform": [
            { "type": "mate" },
            { "type": "filter", "expr": "jexl:get(feature,'score')>=500" }
          ]
        }
      ]
    }
  ]
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "hic_loops",
  "name": "Hi-C loops",
  "uri": "https://example.com/loops.bedpe.gz",
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "color": { "value": "#8b1a1a" }, "strokeWidth": 1 },
          "transform": [
            { "type": "mate" },
            { "type": "filter", "expr": "jexl:get(feature,'\''score'\'')>=500" }
          ]
        }
      ]
    }
  ]
}'

In the app

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",
  "uri": "https://example.com/loops.bedpe.gz",
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "color": { "value": "#8b1a1a" }, "strokeWidth": 1 },
          "transform": [
            { "type": "mate" },
            { "type": "filter", "expr": "jexl:get(feature,'score')>=500" }
          ]
        }
      ]
    }
  ]
}

A strokeWidth bound to a field strokes each loop by its score instead, through a linear or log scale into a range of pixels: Mark display §"Links".

Compartments and subcompartments

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

Config file

Goes in the tracks array of config.json. See Tracks.

{
  "trackId": "hic_compartments",
  "name": "Compartment eigenvector",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "encoding": { "y": { "scale": { "domainMin": -0.03, "domainMax": 0.03 } } }
  }
}

CLI (add-track)

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 '{"encoding":{"y":{"scale":{"domainMin":-0.03,"domainMax":0.03}}}}'

In the app

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:

{
  "trackId": "hic_compartments",
  "name": "Compartment eigenvector",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "encoding": { "y": { "scale": { "domainMin": -0.03, "domainMax": 0.03 } } }
  }
}

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

Config file

Goes in the tracks array of config.json. See Tracks.

{
  "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"
    ]
  }
}

CLI (add-track-json)

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 the app

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
Column nine named itemRgb paints each class in a separate color. 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

Hi-C track

Display settings#

Comparing two conditions#

Loops and interactions as arcs#

Compartments and subcompartments#

See also#

Display settings

Comparing two conditions

Loops and interactions as arcs

Compartments and subcompartments

See also