BAM

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 bam data as seen in VisCom.

Use: Visualizes the aligned reads and assists in understanding depth and quality of genomically mapped features on a nucleotide scale. 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 .bam files they must also have the .bai file associated. What happens is that the ProteinPaint looks for the .bai file and cannot parse the .bam so we must give it an alternate path to the .bai file.

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

{
    "genome": "hg38",
    "nativetracks": "RefGene",
    "position": "chr4:55589607-55590007",
    "block": true,
    "tracks": [
        {
            "type": "bam",
            "name": "Track name",
            "url": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/QGf0F8zB4GYBzPQKg27BvkPgqgk90yqyKfz67gVy\/kit.exon8.del.bam",
            "indexURL": "https:\/\/westus.dl.azure.dnanex.us\/F\/D\/gp8VX25X9YkKvKQqkjvfjPgz834zX51V0x6j7zF0\/kit.exon8.del.bam.bai"
        }
    ]
}

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, and 9

{
    "genome": "hg38",
    "nativetracks": "RefGene",
    "position": "chr4:55589607-55590007",
    "block": true,
    "tracks": [
        {
            "type": "bam",
            "name": "Track name",
            "file": "proteinpaint_demo\/hg19\/bam\/kit.exon8.del.bam"   
        }
    ]
}