Expression Rank

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

Description

These code block examples can be used to generate a gene expression rank track by using a fpkm file 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 Parameter EXAMPLE

warning

If you are using DNAnexus links, be sure to extend the duration. See our manage data section. The sample parameter must be unique to the file otherwise it will not render.

Be sure to update lines 1, 3, 8, 9, 10, and 11

{
    "genome": "hg38",
    "nativetracks": "RefGene",
    "position": "chr8:127340055-128243343",
    "block": true,
    "tracks": [
        {
            "type": "mdsexpressionrank",
            "name": "Track name",
            "url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/X5FV210570zX090JvqJ32kxXX0XxGVyFYP1XbX05\/TCGA.fpkm.gz",
            "indexURL": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/VP5JfbPJKkzBpB5j0KXX33zZfyqjqQjq5VKqXb3J\/TCGA.fpkm.gz.tbi",
            "sample": "TCGA-GS-A9TQ"
        }
    ]
}

Path to file 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, 9, and 10

{
    "genome": "hg38",
    "nativetracks": "RefGene",
    "position": "chr8:127340055-128243343",
    "block": true,
    "tracks": [
        {
            "type": "mdsexpressionrank",
            "name": "Track name",
            "file": "proteinpaint_demo\/hg38\/exprank\/TCGA.fpkm.gz",
            "sample": "TCGA-GS-A9TQ"
        }
    ]
}