JSON BED

Last updated: 3 years ago (view history), Time to read: 1 mins

Description

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

Use: This customizable bed format shows defined genomic regions identified by ChIP seq, mass spec or other means. 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, 8, 9, 10, and 14 

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "bedj",
            "name": "Track name",
            "url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/YpGGYBXzpP05Fyv64G1BjVkgFffp24GxyvYzbZ1F\/gencode.gz",
            "indexURL": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/yf9188G1431Pg6YXkJ07F1238qg5YvF7x3pZfbPx\/gencode.gz.tbi",
            "stackheight": 16,
            "mincutoff": 1,
            "stackspace": 1,
            "color": "teal"
        }
    ]
}

File Key Example

tip

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": "bedj",
            "name": "Track name",
            "file": "proteinpaint_demo\/hg19\/bedj\/gencode.gz",
            "stackheight": 16,
            "mincutoff": 1,
            "stackspace": 1,
            "color": "teal"
        }
    ]
}