Allelic-Imbalance
These code block examples can be used to generate an allelic imbalance figure as seen in VisCom.
These code block examples can be used to generate an allelic imbalance figure as seen in VisCom.
Use: Displays the allelic imbalance of the heterozygous SNP markers in a tumor genome as compared to this patient’s germline genome, as a way of indicating loss of heterozygosity. ProteinPaint Google Docs
URL Key Example
Warning
If you are using DNAnexus links, be sure to extend the duration. See our manage data section. In order to render .gz files they must also have the .tbi file associated. What happens is that the ProteinPaint looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
If you are using DNAnexus links, be sure to extend the duration. See our manage data section. In order to render .gz files they must also have the .tbi file associated. What happens is that the ProteinPaint looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.
Be sure to update lines 1, 3, 8, 9, and 10
{
"genome": "hg19",
"nativetracks": "RefGene",
"position": "chr17:7565096-7590856",
"block": true,
"tracks": [
{
"type": "aicheck",
"name": "Track name",
"url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/zYf5XqZ04fBKk6VbQFQbv8P8BG8xyGyQp3FzFkG8z/\aicheck.gz",
"indexURL": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/b0YJQx5F110Z90P9q7ZZFXqv03Gv41Qfy0yX7gYK/\aicheck.gz.tbi"
}
]
}
File Key Example
Warning
If you are using a path on the HPC, the file must exist in a directory in the
If you are using a path on the HPC, the file must exist in a directory in the
/tp directory.
For more details, see our manage data section.Be sure to update lines 1, 3, 8, and 9
{
"genome": "hg19",
"nativetracks": "RefGene",
"position": "chr17:7565096-7590856",
"block": true,
"tracks": [
{
"type": "aicheck",
"name": "Track name",
"file": "proteinpaint_demo\/hg19\/aicheck\/file.gz"
}
]
}
Learning the Code Block Basics
Our new visualization editor allows you to build visualizations using our new editor interface. The interface prompts certain fields that are required to generate the visualization so you can spend more time exploring and creating visualizations and less time coding.
Arc
These code block examples can be used to generate an arc figure as seen in VisCom.