Visualization Community | St. Jude Cloud

GenomePaint Hi-C Example

Zhou Lab

Sep 28, 2021

3.5K

Hi-C

Visualize Juicebox .hic files from Hi-C experiments. The Hi-C track also supports a whole genome view, example here. Learn more about the Hi-C track.

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runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "mm9",
  position: "chr7:13749862-20841903",
  nativetracks: "RefGene",
  tracks: [
    {
      "type": "hicstraw",
      "file": "proteinpaint_demo/mm9/hic/hic_demo.hic",
      "name": "Example Hi-C",
      "percentile_max": 95,
      "mincutoff": 1,
      "pyramidup": 1,
      "enzyme": "MboI",
    },
  ]
});

Visualization Code

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "mm9",
  position: "chr7:13749862-20841903",
  nativetracks: "RefGene",
  tracks: [
    {
      "type": "hicstraw",
      "file": "proteinpaint_demo/mm9/hic/hic_demo.hic",
      "name": "Example Hi-C",
      "percentile_max": 95,
      "mincutoff": 1,
      "pyramidup": 1,
      "enzyme": "MboI",
    },
  ]
});

GenomePaint Hi-C Example

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Visualization Code