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igv-manual-counts.html
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igv-manual-counts.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta content="Jim Robinson" name="author">
<link href=img/favicon.ico rel="shortcut icon">
<title>igv.js</title>
</head>
<body>
<h1>IGV.js alignment</h1>
<div id="igv-div" style="padding-top: 10px;padding-bottom: 10px; border:1px solid lightgray"></div>
<script type="module">
import igv from "https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/igv.esm.min.js"
var igvDiv = document.getElementById("igv-div");
var options = {
genome: {
id: "hg38 (Ensemble release 109)",
fastaURL: "https://bioinformatics.erc.monash.edu/home/andrewperry/tmp/hg38/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz",
indexURL: "https://bioinformatics.erc.monash.edu/home/andrewperry/tmp/hg38/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz.fai",
},
tracks: [
{
name: "Genes",
type: "annotation",
format: "gtf",
// url: "https://bioinformatics.erc.monash.edu/home/andrewperry/tmp/hg38/Homo_sapiens.GRCh38.109.sorted.gtf",
url: "https://bioinformatics.erc.monash.edu/home/andrewperry/tmp/hg38/Homo_sapiens.GRCh38.109.sorted.gtf.gz",
indexURL: "https://bioinformatics.erc.monash.edu/home/andrewperry/tmp/hg38/Homo_sapiens.GRCh38.109.sorted.gtf.gz.tbi",
displayMode: "EXPANDED",
searchable: true
},
{
name: "SRR2155413 Alignments",
type: "alignment",
format: "bam",
url: "https://bioinformatics.erc.monash.edu/home/andrewperry/tmp/3lQ6tw48pcFfOKyg1vTJry/output/results/star_salmon/SRR2155413.markdup.sorted.bam",
indexURL: "https://bioinformatics.erc.monash.edu/home/andrewperry/tmp/3lQ6tw48pcFfOKyg1vTJry/output/results/star_salmon/SRR2155413.markdup.sorted.bam.bai"
}
]
};
igv.createBrowser(igvDiv, options)
.then(function (browser) {
console.log("IGV browser created");
})
.catch(function (error) {
console.error(error);
});
</script>
</body>
</html>