input.yaml

OUTPUT_FOLDER_PATH: "/Users/ilaigenishmac/CS/enrichment/Zohar-Projects/Iceberg-project/TIGIT-REP2-RESULTS-TESTS/"


ANALYZER STEPS:
    UMI: True
    EXPERIMENT_LIBRARIES_DETECTION: True
    EXPERIMENT_TRACES_REMOVAL: True
    BWA: True
    UNITE_READS_TO_ICEBERGS: True
    MERGE_TREATMENT_AND_CONTROL_ICEBERGS_BY_LOCUS: True
    UNITE_CLOSE_ICEBERGS_SITES: True
    BREAKS_CLASSIFY: True
    CALCULATE_ICEBERGS_SITES_PROFILE: True
    GUIDERNA_ALIGNMENT: True
    REPORTS: True



EXPERIMENTS:
    GENERAL:
        REFERENCE_GENOME_PATH: "/Users/ilaigenishmac/CS/enrichment/Zohar-Projects/Iceberg-project/genome/hg38.fa"
        EXPERIMENTS_TAG: "GTTTAATTGAGTTGTCATATGTTAATAACGGTAT"

    TX:
        NAME: "TIGIT-2"
        EXPERIMENT_FOLDER_PATH: "/Users/ilaigenishmac/CS/enrichment/Zohar-Projects/Iceberg-project/omri_panels-19.10.21/EXPERIMENTS-FILES/TIGIT-2_18-4-21/"
        R1: "TIGIT-2_S16_R1_001.fastq"
        R2: "TIGIT-2_S16_R2_001.fastq"
        I1: "TIGIT-2_S16_I1_001.fastq"
        I2: "TIGIT-2_S16_I2_001.fastq"
        GUIDERNA: "GCCCCTGGGCCCAGATCAGG"
    
    CONTROL:
        NAME: "CONTROL"
        EXPERIMENT_FOLDER_PATH: "/Users/ilaigenishmac/CS/enrichment/Zohar-Projects/Iceberg-project/omri_panels-19.10.21/EXPERIMENTS-FILES/TIGIT-2_18-4-21/"
        R1: "Mock-1_S1_R1_001.fastq"
        R2: "Mock-1_S1_R2_001.fastq"
        I1: "Mock-1_S1_I1_001.fastq"
        I2: "Mock-1_S1_I2_001.fastq"



HYPERPARAMATERS:
    UMI_BPS_AMOUNT_FROM_READS_START: 6
    MIN_QUALITY: 10
    MIN_FREQUENCY: 0.6
    MAX_READS_DISTANCE: 400
    MAX_ICEBERG_DISTANCE: 0
    MAX_ALIGNMENTS_HAMMING_DISTANCE: 5
    NOISE_BINS_AND_CONTROL_MAPQ_PERCENTILE: [[[0, 1], 0.5, 10],
                                             [[1, 50], 0.5, 10],
                                             [[50, 61], 0.5, 10]]
    CRISPR_ACTIVITY_THRESHOLD: 0.9



# bwa: /Users/ilaigenishmac/CS/enrichment/Zohar-Projects/Iceberg-project/bwa-0.7.17/bwa
# bedtools: bedtools