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| color: $igv-dark-grey-color; | ||
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| width: 95%; | ||
| height: 24px; | ||
| line-height: 24px; | ||
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| text-align: left; | ||
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| @@ -0,0 +1,74 @@ | ||
| <!DOCTYPE html> | ||
| <html lang="en"> | ||
| <head> | ||
| <meta charset="UTF-8"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1.0"> | ||
| <title>Git Issue - 1886</title> | ||
| </head> | ||
| <body> | ||
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| <header> | ||
| <h1>Git Issue - 1886</h1> | ||
| </header> | ||
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| <main> | ||
| <div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div> | ||
| </main> | ||
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| <script type="module"> | ||
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| import igv from "../../js/index.js" | ||
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| const config = | ||
| { | ||
| "version": "3.0.5", | ||
| "showSampleNames": false, | ||
| "reference": { | ||
| "id": "hg19", | ||
| "name": "Human (GRCh37/hg19)", | ||
| "fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta", | ||
| "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta.fai", | ||
| "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz", | ||
| "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chromAlias.txt", | ||
| "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit", | ||
| "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes", | ||
| "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" | ||
| }, | ||
| "locus": "chr3:86,924,605-86,924,924", | ||
| "roi": [], | ||
| "tracks": [ | ||
| { | ||
| "type": "sequence", | ||
| "order": -9007199254740991 | ||
| }, | ||
| { | ||
| "sourceType": "gcs", | ||
| "type": "alignment", | ||
| "url": "gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam", | ||
| "indexURL": "gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam.bai", | ||
| "name": "NA12889", | ||
| "order": 0, | ||
| "colorBy": "unexpectedPair" | ||
| }, | ||
| { | ||
| "name": "Refseq Genes", | ||
| "format": "refgene", | ||
| "id": "hg19_genes", | ||
| "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz", | ||
| "indexed": false, | ||
| "order": 1000000, | ||
| "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$", | ||
| "type": "annotation", | ||
| "height": 70 | ||
| } | ||
| ] | ||
| } | ||
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| igv.createBrowser(document.getElementById('igvDiv'), config) | ||
| .then(browser => { | ||
| console.log(`browser ${ browser.guid } is good to go`) | ||
| }) | ||
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| </script> | ||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| { | ||
| "version": "2.16.0", | ||
| "showSampleNames": false, | ||
| "sampleNameViewportWidth": 6, | ||
| "genome": "hg38", | ||
| "locus": "chr6:152,971,612-152,992,127", | ||
| "roi": [], | ||
| "sampleinfo": [ | ||
| { | ||
| "type": "sampleinfo", | ||
| "url": "https://www.dropbox.com/s/oeg6y37mvyfjif3/sampleInfo.txt?dl=0" | ||
| } | ||
| ], | ||
| "tracks": [ | ||
| { | ||
| "url": "https://www.dropbox.com/scl/fi/9begjuwqq1kwhcbtnrioq/model2.allChr.f.2.hg38.r10-Yan-Hu.hic?rlkey=n94vc1qvlsn19fjocki9ereff&dl=0", | ||
| "filename": "model2.allChr.f.2.hg38.r10-Yan-Hu.hic", | ||
| "name": "m", | ||
| "order": 0, | ||
| "format": "hic", | ||
| "type": "shoebox", | ||
| "displayMode": "SQUISHED", | ||
| "height": 500, | ||
| "visibilityWindow": 1000000 | ||
| } | ||
| ] | ||
| } |
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