Troubleshooting barcode classification issues

Use the BaseCaller JSON output file to troubleshoot barcode classification issues. Barcode classification metrics are available in the basecaller_results/datasets_basecaller.json file in the Torrent Suite™ Software analysis directory. This file contains information about all barcodes, whether they appear in the run report or are filtered out.

A sample of this file is shown here, and is used in later examples.

{
    "0NCWC.IonHDdual_0101": {
        "Q20_bases": 25,
        "barcode": {
           "barcode_adapter": "",
            "barcode_adapter_filtered": 0,
            "barcode_bias": [
                0.209209978580475,
                -0.0654730796813965,
                -0.0002632737159729,
                0.0154760638251901,
                0.177288889884949,
                0.2724369764328,
                0.00381212681531906,
                0.105516441166401,
                -0.292163729667664,
                0.0684881433844566,
                -0.000637046992778778,
                -0.0821478366851807,
                -0.0467215031385422,
                0.0904117226600647
            ],
            "barcode_distance_hist": [
                0,
                1,
                0,
                0,
                0
            ],
            "barcode_errors_hist": [
                1,
                0,
                0
            ],
            "barcode_match_filtered": 0,
            "barcode_name": "IonHDdual_0101",
            "barcode_sequence": "CTAAGGTAAC"
        },
        "barcode_name": "IonHDdual_0101",
        "description": "KHAresPanV5bidirhUnewdesignMETCNVladder3",
        "end_barcode": {
            "adapter_filtered": 0,
            "barcode_adapter": "",
            "barcode_errors_hist": [
                1,
                0,
                0,
                0
            ],
            "barcode_filtered": 757,
            "barcode_name": "IonHDdual_0101",
            "barcode_sequence": "TGACTCTATTCG",
            "no_bead_adapter": 17
        },
        "filtered": true,
        "handle": {
            "bc_handle_distribution": [
                0,
                1,
                0
            ],
            "bc_handle_errors_hist": [
                1,
                0,
                0,
                0
            ],
            "bc_handle_filtered": 82,
            "end_handle_distribution": [
                0,
                0,
                1
            ],
            "end_handle_errors_hist": [
                1,
                0,
                0,
                0
            ],
            "end_handle_filtered": 0
        },
        "index": 1,
        "mol_tag_prefix": "TNNNACTNNNTGAT",
        "mol_tag_suffix": "ATCANNNAGTNNNA",
        "num_blocks_filtered": 96,
        "platform_unit": "s5/540/QPT035/18/DADL00693/IonHDdual_0101",
        "read_count": 1,
        "reference": "hg19",
        "sample": "none",
        "total_bases": 25
    }
}