Barcode Details Json

The Barcode Details Json provides callingCardsTools with information about what and where to expect non-genomic sequence which are included in the raw reads and serve to both demultiplex, in the case of yeast data, and confirm that a given read represents a transposon insertion.

The mammals data barcode details is generally static – you can use the same barcode details for all data. However, the yeast barcode details must be adjusted for each specific library.

Yeast Barcode Details Format

It is most convenient to store the TF barcode sequences as a tsv and then use the cmd line tool callingcardstools barcode_table_to_json to convert the table to the appropriate json template.

Save a tsv in the following format: Do not include a header

MTH1	GTCCC	CAGAGGGG
SKN7	TCAAG	ATCAGACC
HAP3	AATGA	GGGGGTAG

The output of

callingcardstools barcode_table_to_json -t run_6354_bc_table.tsv -r run_6354

will be a json in the following format:

{
    "r1": {
        "primer": {
            "trim": true,
            "index": [
                0,
                5
            ]
        },
        "transposon": {
            "trim": true,
            "index": [
                5,
                22
            ]
        }
    },
    "r2": {
        "transposon": {
            "trim": true,
            "index": [
                0,
                8
            ]
        },
        "restriction": {
            "trim": true,
            "index": [
                8,
                20
            ]
        }
    },
    "components": {
        "r1_transposon": {
            "map": [
                "AATTCACTACGTCAACA"
            ],
            "bam_tag": "RT"
        },
        "r2_restriction": {
            "map": {
                "TCGAGCGCCCGG": "Hpall",
                "TCGAGCGC": "HinP1I",
                "TCGA": "TaqAI"
            },
            "match_type": "greedy",
            "require": false,
            "bam_tag": "RS"
        },
        "tf": {
            "components": [
                "r1_primer",
                "r2_transposon"
            ],
            "map": {
                "GTCCCCAGAGGGG": "MTH1",
                "TCAAGATCAGACC": "SKN7",
                "AATGAGGGGGTAG": "HAP4"
            },
            "bam_tag": "TF"
        }
    },
    "match_allowance": {
        "r1_transposon": 0
    },
    "batch": "run_6354"
}

Mammals Barcode Details Format

Since this will generally be the same for all mammals Calling Cards data, you can likely simply copy and paste this onto your system and use it directly:

{
    "batch": "",
    "tf": "",
    "r1": {
        "pb": {"trim": true,
               "index": [0,3]},

        "ltr1": {"trim": true,
                    "index": [3,28]},
        "srt": {"trim": true,
                "index":[28,32]},

        "ltr2": {"trim": true,
                    "index": [32,38]}
    },
    "r2":{},
    "components": {

        "r1_pb":    {"map":["TAG"],
                     "match_allowance": 0,
                     "bam_tag": "PB"},

        "r1_ltr1":  {"map": ["CGTCAATTTTACGCAGACTATCTTT"],
                     "match_type": "edit_distance",
                     "match_allowance": 0,
                     "require": true,
                     "bam_tag": "L1"},
        "r1_srt":   {"map": ["CTAG", "CAAC", "CTGA", "GCAT", "GTAC", "CACA", "TGAC", "GTCA",
                             "CGAT", "CTCT", "GAAG", "TCGA", "CATG", "GTTG", "CTTC", "GCTA",
                             "GAGA", "GTGT", "CGTA", "TGGT", "GGAA", "ACAC", "TCAG", "TTGG",
                             "CAGT", "TTTT"],
                     "match_type": "edit_distance",
                     "match_allowance": 0,
                     "require": true,
                     "bam_tag": "ST",
                     "annotation": true},
        "r1_ltr2":  {"map": ["GGTTAA"],
                     "match_type": "edit_distance",
                     "match_allowance": 0,
                     "require": true,
                     "bam_tag": "L2"}
    },
    "insert_seq": ["TTAA"],
    "max_mismatch": 0
}