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GenomePaint Allele-specific expression (ASE) Example - beta

Zhou Lab

Sep 28, 2021

3.7K

RNA Sequencing

The allele-specific expression (ASE) track annotates the tumor gene expression. Scroll through the color coded FPKM values on the right to reveal the ASE status: mono-allelic, bi-allelic, uncertain, or no information available. Clicking on the DNA markers represented as 'x's, generates a pop-up of the marker details, sample view in the genome brower, and a diverging stacked bar chart of the transcript factor motif.

Learn more about the ASE track

Loading Visualization

runproteinpaint({
	holder:document.getElementById('visualization_container'),
	host:'https://proteinpaint.stjude.org',
	parseurl:true,
	nobox:1,
	block:1,
	noheader:1,
	position:'chr5:1252462-1297568',
	genome:'hg38',
	nativetracks:'refgene',
	tracks:[
		{
			type:'mdssvcnv',
			name:'Demo ASE',
			checkvcf:{
				file:'proteinpaint_demo/hg38/ase/vcf.gz',
			},
			checkrnabam:{
				hetsnp_minbaf:0.2,
				hetsnp_maxbaf:0.8,
				samples:{
					sample1: {
						file: "proteinpaint_demo/hg38/ase/sample1.bam",
						totalreads: 172048689,
						pairedend: true
					},
					sample2: {
						file: 'proteinpaint_demo/hg38/ase/sample2.bam',
						totalreads: 151710239,
						pairedend: true
					},
					sample3: {
						file: 'proteinpaint_demo/hg38/ase/sample3.bam',
						totalreads: 167864903,
						pairedend: true
					},
					sample4: {
						file: 'proteinpaint_demo/hg38/ase/sample4.bam',
						totalreads: 153196442,
						pairedend: true
					},
					sample12:{
						file: 'proteinpaint_demo/hg38/ase/sample12.bam',
						totalreads: 155650314,
						pairedend: true
					},
					sample5: {
						file: 'proteinpaint_demo/hg38/ase/sample5.bam',
						totalreads: 144649042,
						pairedend: true
					},
					sample6: {
						file: 'proteinpaint_demo/hg38/ase/sample6.bam',
						totalreads: 170516947,
						pairedend: true
					},
					sample7: {
						file: 'proteinpaint_demo/hg38/ase/sample7.bam',
						totalreads: 167971047,
						pairedend: true
					},
					sample8: {
						file: 'proteinpaint_demo/hg38/ase/sample8.bam',
						totalreads: 137990338,
						pairedend: true
					},
					sample9: {
						file: 'proteinpaint_demo/hg38/ase/sample9.bam',
						totalreads: 150401722,
						pairedend: true
					},
					sample10: {
						file: 'proteinpaint_demo/hg38/ase/sample10.bam',
						totalreads: 131681552,
						pairedend: true
					},
					sample11: {
						file: 'proteinpaint_demo/hg38/ase/sample11.bam',
						totalreads: 150240544,
						pairedend: true
					},
				},
			}
		},
	]
})

runproteinpaint({
	holder:document.getElementById('visualization_container'),
	host:'https://proteinpaint.stjude.org',
	parseurl:true,
	nobox:1,
	block:1,
	noheader:1,
	position:'chr5:1252462-1297568',
	genome:'hg38',
	nativetracks:'refgene',
	tracks:[
		{
			type:'ase',
			name:'Demo ASE',
			vcffile:'proteinpaint_demo/hg38/ase/vcf.gz',
			hetsnp_minbaf:0.1,
			hetsnp_maxbaf:0.8,
			samplename:'sample12',
			rnabamfile: 'proteinpaint_demo/hg38/ase/sample12.bam',
			rnabamtotalreads: 155650314,
			checkrnabam:{
				hetsnp_minbaf:.2,
				hetsnp_maxbaf:.8
			}
		}
	]
})

Visualization Code

runproteinpaint({
	holder:document.getElementById('visualization_container'),
	host:'https://proteinpaint.stjude.org',
	parseurl:true,
	nobox:1,
	block:1,
	noheader:1,
	position:'chr5:1252462-1297568',
	genome:'hg38',
	nativetracks:'refgene',
	tracks:[
		{
			type:'mdssvcnv',
			name:'Demo ASE',
			checkvcf:{
				file:'proteinpaint_demo/hg38/ase/vcf.gz',
			},
			checkrnabam:{
				hetsnp_minbaf:0.2,
				hetsnp_maxbaf:0.8,
				samples:{
					sample1: {
						file: "proteinpaint_demo/hg38/ase/sample1.bam",
						totalreads: 172048689,
						pairedend: true
					},
					sample2: {
						file: 'proteinpaint_demo/hg38/ase/sample2.bam',
						totalreads: 151710239,
						pairedend: true
					},
					sample3: {
						file: 'proteinpaint_demo/hg38/ase/sample3.bam',
						totalreads: 167864903,
						pairedend: true
					},
					sample4: {
						file: 'proteinpaint_demo/hg38/ase/sample4.bam',
						totalreads: 153196442,
						pairedend: true
					},
					sample12:{
						file: 'proteinpaint_demo/hg38/ase/sample12.bam',
						totalreads: 155650314,
						pairedend: true
					},
					sample5: {
						file: 'proteinpaint_demo/hg38/ase/sample5.bam',
						totalreads: 144649042,
						pairedend: true
					},
					sample6: {
						file: 'proteinpaint_demo/hg38/ase/sample6.bam',
						totalreads: 170516947,
						pairedend: true
					},
					sample7: {
						file: 'proteinpaint_demo/hg38/ase/sample7.bam',
						totalreads: 167971047,
						pairedend: true
					},
					sample8: {
						file: 'proteinpaint_demo/hg38/ase/sample8.bam',
						totalreads: 137990338,
						pairedend: true
					},
					sample9: {
						file: 'proteinpaint_demo/hg38/ase/sample9.bam',
						totalreads: 150401722,
						pairedend: true
					},
					sample10: {
						file: 'proteinpaint_demo/hg38/ase/sample10.bam',
						totalreads: 131681552,
						pairedend: true
					},
					sample11: {
						file: 'proteinpaint_demo/hg38/ase/sample11.bam',
						totalreads: 150240544,
						pairedend: true
					},
				},
			}
		},
	]
})

runproteinpaint({
	holder:document.getElementById('visualization_container'),
	host:'https://proteinpaint.stjude.org',
	parseurl:true,
	nobox:1,
	block:1,
	noheader:1,
	position:'chr5:1252462-1297568',
	genome:'hg38',
	nativetracks:'refgene',
	tracks:[
		{
			type:'ase',
			name:'Demo ASE',
			vcffile:'proteinpaint_demo/hg38/ase/vcf.gz',
			hetsnp_minbaf:0.1,
			hetsnp_maxbaf:0.8,
			samplename:'sample12',
			rnabamfile: 'proteinpaint_demo/hg38/ase/sample12.bam',
			rnabamtotalreads: 155650314,
			checkrnabam:{
				hetsnp_minbaf:.2,
				hetsnp_maxbaf:.8
			}
		}
	]
})

GenomePaint Allele-specific expression (ASE) Example - beta

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Visualization Code