BigWig Stranded

Last updated: 3 years ago (view history), Time to read: 2 mins

Description

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

Use: RNA-seq coverage data as a pair of bigWig tracks, with forward strand on top and reverse strand on bottom. 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, 10, and 13

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "bigwigstranded",
            "name": "Track name",
            "strand1": {
                "url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/1jG5YJYqxpQqz9JQx6xzJVV2J23p0jG5Bp9f60BJ\/sense.bw"
            },
            "strand2": {
                "url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/JK7j09Bb0P33fZ0KFvJ07Gx292BQpXb95kZ2K87X\/antisense.bw",
                "normalize": {
                    "dividefactor": -1
                }
            }
        }
    ]
}

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.

Be sure to update lines 1, 3, 8, 10, and 13

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "bigwigstranded",
            "name": "Track name",
            "strand1": {
                "file": "proteinpaint_demo\/hg19\/strandedbigwig\/sense.bw"   
            },
            "strand2": {
                "file": "proteinpaint_demo\/hg19\/strandedbigwig\/antisense.bw",   
                "normalize": {
                    "dividefactor": -1
                }
            }
        }
    ]
}