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| <head> | ||
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| <link rel="stylesheet" href="https://unpkg.com/@reservoirgenomics/[email protected]/dist/hglib.css"> | ||
| <script crossorigin src="https://unpkg.com/[email protected]/dist/higlass-plugins.min.js"> | ||
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| </script> | ||
| <script crossorigin src="https://unpkg.com/@reservoirgenomics/[email protected]/dist/hglib.js"> | ||
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| </script> | ||
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| <meta charset="UTF-8"/> | ||
| <meta http-equiv="X-UA-Compatible" content="IE=edge"/> | ||
| <title>Juicebox</title> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1.0"/> | ||
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| <!-- Font Awesome CSS--> | ||
| <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css"> | ||
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| <!-- Juicebox CSS--> | ||
| <link rel="stylesheet" type="text/css" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/juicebox.css"> | ||
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| <!-- Juicebox JS --> | ||
| <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/juicebox.js"></script> | ||
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| <!-- IGV JS --> | ||
| <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.min.js"></script> | ||
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| </head> | ||
| <body> | ||
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| <div id="igv-container" style="width: auto; margin-left: 10px; border: 1px solid black;"> | ||
| </div> | ||
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| <div id="juicebox-container" style="margin-top: 20px; margin-left: 10px;display:inline-flex;"> | ||
| </div> | ||
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| <script> | ||
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| const juiceboxConfig = | ||
| { | ||
| browsers: [ | ||
| { | ||
| genome: "hg38", | ||
| url: "https://www.encodeproject.org/files/ENCFF020DPP/@@download/ENCFF020DPP.hic", | ||
| name: "HepG2 HiC", | ||
| locus: "chr1:19,150,000-19,250,000", | ||
| //normalization: "SCALE", | ||
| //resolution: 1000 | ||
| }, | ||
| { | ||
| genome: "hg38", | ||
| url: "https://www.encodeproject.org/files/ENCFF020DPP/@@download/ENCFF020DPP.hic", | ||
| name: "HepG2 HiC", | ||
| locus: "chr1:19,150,000-19,250,000", | ||
| //normalization: "SCALE", | ||
| //resolution: 1000 | ||
| } | ||
| ] | ||
| } | ||
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| juicebox.init(document.getElementById("juicebox-container"), juiceboxConfig) | ||
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| </script> | ||
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| <script> | ||
| const igvConfig = | ||
| { | ||
| genome: "hg38", | ||
| locus: "chr1:19,150,000-19,250,000", | ||
| tracks: [ | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF004DTQ/@@download/ENCFF004DTQ.bigWig", | ||
| name: "HepG2 miRNA (plus strand)", | ||
| color: "rgb(200,0,0)", | ||
| format: "bigwig", | ||
| type: "wig", | ||
| flipAxis: true | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF646XYR/@@download/ENCFF646XYR.bigWig", | ||
| name: "HepG2 miRNA (minus strand)", | ||
| color: "rgb(200,0,0)", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF908VIH/@@download/ENCFF908VIH.bigWig", | ||
| name: "HepG2 total RNA-seq (plus strand)", | ||
| color: "rgb(0,200,0)", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF991LOA/@@download/ENCFF991LOA.bigWig", | ||
| name: "HepG2 total RNA-seq (minus strand)", | ||
| color: "rgb(0,200,0)", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF285FQS/@@download/ENCFF285FQS.bigWig", | ||
| name: "HepG2 ATAC-seq", | ||
| color: "rgb(200,0,150)", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF645ZUY/@@download/ENCFF645ZUY.bigWig", | ||
| name: "HepG2 H3K4me3", | ||
| color: "rgb(200,0,150)", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF113VII/@@download/ENCFF113VII.bigWig", | ||
| name: "HepG2 H3K27ac", | ||
| color: "rgb(200,0,150)", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF113VII/@@download/ENCFF113VII.bigWig", | ||
| name: "HepG2 DNase-seq", | ||
| color: "rgb(200,0,150)", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF364UNM/@@download/ENCFF364UNM.bedpe.gz", | ||
| type: "interact", | ||
| format: "bedpe", | ||
| name: "HepG2 POLR2A ChIA-PET", | ||
| arcType: "nested", | ||
| color: "rgb(0,0,150)", | ||
| showBlocks: true, | ||
| visibilityWindow: 10000000, | ||
| height: 100 | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF299NHM/@@download/ENCFF299NHM.bedpe.gz", | ||
| type: "interact", | ||
| format: "bedpe", | ||
| name: "HepG2 CTCF ChIA-PET", | ||
| arcType: "nested", | ||
| color: "rgb(0,0,150)", | ||
| showBlocks: true, | ||
| visibilityWindow: 10000000, | ||
| height: 100 | ||
| }, | ||
| { | ||
| url: "https://www.encodeproject.org/files/ENCFF545CMV/@@download/ENCFF545CMV.bigWig", | ||
| name: "HepG2 genome compartments", | ||
| format: "bigwig", | ||
| type: "wig" | ||
| } | ||
| ] | ||
| } | ||
| igv.createBrowser(document.getElementById("igv-container"), igvConfig) | ||
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| </script> | ||
| </body> |