{ 
    "chic_reference_file"  :  "/hpc/hub_oudenaarden/group_references/ensembl/97/homo_sapiens/primary_assembly.fasta",
    "trans_reference_file"  :  "/hpc/hub_oudenaarden/group_references/ensembl/97/homo_sapiens/NOMASK_ribo_star_index_120",
    "reference_fasta"  :  "/hpc/hub_oudenaarden/group_references/ensembl/97/homo_sapiens/primary_assembly_NOMASK_ERCC92_ribo.fa",
    "introns" : "/hpc/hub_oudenaarden/group_references/ensembl/97/homo_sapiens/introns.gtf.gz",
    "exons" : "/hpc/hub_oudenaarden/group_references/ensembl/97/homo_sapiens/exons.including_ribo.gtf.gz",
    "blacklist" : "/hpc/hub_oudenaarden/bdebarbanson/ref/500_plus_coverage_spikes_blacklist_CHiC_mm10.bed",
    "counting_min_mq" : 50,
    "counting_bin_sizes": [50_000],
    "chic_mapper":"bwa",
    "trans_mapper":"STAR",
    "plot_bin_sizes" : [500_000, 1000_000],
    "4sU":"disabled",
    "known_variants":"/hpc/hub_oudenaarden/group_references/ensembl/97/homo_sapiens/all_snps.vcf.gz"
}