index.md

title
BAM

Description

These code block examples can be used to generate a figure using bam data as seen in VisCom.

Use: sequence reads alignment ProteinPaint Google Docs

URL Key Example

Be sure to update lines 8, 9, 14 and 15

runproteinpaint({   
	host:'https://proteinpaint.stjude.org',
	holder: document.getElementById("#visualization_container"),
	parseurl:true,
	block: true,
	nobox:1,
	noheader:1,
	genome:'hg19',
	position:'chr4:55589707-55589907',
	nativetracks:'RefGene',
	tracks:[   
		{
			type:'bam',
			url:'enter link here',
			name:'name of track',
		}
	]
})

File Key Example

Be sure to update lines 8, 9, 14 and 15

runproteinpaint({   
	host:'https://proteinpaint.stjude.org',
	holder: document.getElementById("#visualization_container"),
	parseurl:true,
	block: true,
	nobox:1,
	noheader:1,
	genome:'hg19',
	position:'chr4:55589707-55589907',
	nativetracks:'RefGene',
	tracks:[   
		{
			type:'bam',
			file:'paste name/path_to_file/.bam',
			name:'name of track',
		}
	]
})