Herring-Project/salmon_code at master · WhiteheadLab/Herring-Project · GitHub

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#example of salmon quant file generation for a single sample
{
    "salmon_version": "1.3.0",
    "index": "/home/jagill/CP_ref_transcriptome/pacherring4_pcbio_idx",
    "libType": "IU",
    "mates1": [
        "93_S114_L004_R1_001_paired.fastq.gz",
        "93_S110_L006_R1_001_paired.fastq.gz",
        "93_S110_L007_R1_001_paired.fastq.gz",
        "93_S110_L008_R1_001_paired.fastq.gz"
    ],
    "mates2": [
        "93_S114_L004_R2_001_paired.fastq.gz",
        "93_S110_L006_R2_001_paired.fastq.gz",
        "93_S110_L007_R2_001_paired.fastq.gz",
        "93_S110_L008_R2_001_paired.fastq.gz"
    ],
    "allowDovetail": [],
    "validateMappings": [],
    "seqBias": [],
    "output": "/home/jagill/results/oil18/prjct1_plate4/quant4/CP-D6-H4A",
    "auxDir": "aux_info"