Hi-C

Last updated: 2 years ago (view history), Time to read: 2 mins

Description

These code block examples can be used to generate a heatmap as seen in VisCom.

Use: The standard Hi-C visualization for chromatin conformation data highlighting observed linkages between distant genomic regions. ProteinPaint Google Docs

URL Key Example

warning

If you are using DNAnexus links, be sure to extend the duration. See our manage data section.

Be sure to update lines 1, 3, 9, and 13

JS

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "hicstraw",
            "name": "Track name",
            "url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/qJzQ6J0BVVQGP57F0Q2b2x2BFKJVQqpxP76g8BYY\/hic_Nalm6.inter.hic",
            "percentile_max": 95,
            "mincutoff": 1,
            "pyramidup": 1,
            "enzyme": "MboI"
        }
    ]
}

File Key Example

warning

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. percentile_max is for the resolution of the Hi-C plot. pyramidup must be 1 to be upward or 0 for downward. enzyme is the restriction enzyme used to cut. .gz and .tbi files are not accepted for Hi-C at this time.

Be sure to update lines 1, 3, 8, and 9 

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "hicstraw",
            "name": "Track name",
            "file": "proteinpaint_demo\/hg19\/hic\/hic_demo.hic",
            "percentile_max": 95,
            "mincutoff": 1,
            "pyramidup": 1,
            "enzyme": "MboI"
        }
    ]
}