RNA Splice Junction

Last updated: 2 years ago (view history), Time to read: 1 mins

Description

These code block examples can be used to generate a RNA splice junction from a cohort as seen in Viscom.

Use: This visualization displays the number of mapped junction reads precisely along with a gene model and will include alternative splicing and isoforms if available. ProteinPaint Google Docs

warning

If you are using DNAnexus links, be sure to extend the duration. See our manage data section. In order to render .gz files they must also have the .tbi file associated. What happens is that the runproteinpaint() looks for the .tbi file and cannot parse the .gz so we must give it an alternate path to the .tbi file.

URL Parameter EXAMPLE

This currently is not supported with a url key at this time.

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.

Path to file EXAMPLE

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

{
    "genome": "hg19",
    "nativetracks": "RefGene",
    "position": "chr17:7565096-7590856",
    "block": true,
    "tracks": [
        {
            "type": "junction",
            "name": "Track name",
            "file": "proteinpaint_demo\/hg19\/junction\/file.gz"
        }
    ]
}