enhancers /grid/gillis/data/lohia/ABC-GWAS-Paper/comparePredictorsToCRISPRData/predictions/ABC/hglft_genome_19_to_38_all_enhancer_K562.bed
genes /grid/gillis/data/lohia/ABC-Enhancer-Gene-Prediction/reference/hg38/RefSeqCurated.170308.bed.CollapsedGeneBounds.hg38.bed
outdir myout_custom
window 5000000
score_column ABC.Score
threshold 0.02
cellType K562
chrom_sizes None
HiCdir /grid/gillis/data/lohia/hi_c_data_processing/data_human/aggregates/5kbp_raw
hic_resolution 5000
tss_hic_contribution 100
hic_pseudocount_distance 1000000.0
hic_type bedpe
hic_is_doubly_stochastic False
scale_hic_using_powerlaw True
hic_gamma 0.87
hic_gamma_reference 0.87
run_all_genes False
expression_cutoff 1
promoter_activity_quantile_cutoff 0.4
make_all_putative True
use_hdf5 False
tss_slop 500
chromosomes all
include_chrY False