config.json

{
  "PATHS":{
    "GENOME": "data/Homo_sapiens.GRCh38.dna.primary_assembly.fa",
    "ANNOTATIONS": "data/Homo_sapiens.GRCh38.112.gtf",
    "ESSENTIALITY": "data/HAP1_essentiality_Toronto.tsv",
    "EXPRESSION": "data/gene_expression_table.tsv",
    "ACCESSIBILITY": "",
    "RESULTS": "results"
  },
  
  "CHROMOSOMES": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"],
  "MOTIFS": ["AAG", "CTT"],

  "GENE_ESSENTIALITY_THRESHOLD": -2,
  "FILTER_GENES_CUTOFF": 100,

  "SEARCH_WINDOW_UPSTREAM_SIZE_MAX": 100000,
  "SEARCH_WINDOW_DOWNSTREAM_SIZE_MAX": 100000,
  "GUIDE_LENGTH": 30,

  "GENE_METRIC_COLUMNS": ["gene", "seqname", "start", "end", "size", "strand", "nearest_upstream_name", "nearest_downstream_name", "lfc", "HEK293T_D2_R1", "HEK293T_D2_R2", "HEK293T_D2-F3_R1", "HEK293T_D2-G5_R1", "HAP1_c12_R1",	"HAP1_c12_R2", "HAP1_c12-B1_R1", "HAP1_c12-C5_R1", "HAP1_c516_R1", "HAP1_c516_R2", "HEK293T_PE2_R1", "HEK293T_PE2_R2", "HEK293T_PE2peg_R1", "HEK293T_PE2peg_R2", "HAP1_OTX2_dE1234567_1", "HAP1_OTX2_dE1234567_2", "HAP1_OTX2_unscr_1", "HAP1_c12-C5_R2"],
  "MOTIF_METRIC_COLUMNS": []
}