config.txt

#### File Path #####
file_path=/home/fuyao/FunSeq_PCAWG/data_context

#### 1000G SNP file ####
tgp_snp=1kg.phase1.snp.bed.gz

#### GERP file ####
gerp_file=All_hg19_RS.bw

#### Sensitive region ####
sensitive=sensitive.nc.bed

#### Ultra conserved region ####
conserved=ultra.conserved.hg19.bed

#### Genome annotations ####
encode_annotation=new_ENCODE.gz

#### Bound motif file ####
bound_motif=ENCODE.tf.bound.union.bed.gz

#### HOT region file (highly occupied regions) ####
hot_file=hot_region.bed

#### Enhancer-gene pairs #####
enhancer=drm.gene.new.bed

#### Motif PWM file ####
motif_pfm=motif.PFM

#### Motif score file ####
score_file=motif.score.cut

#### Network file path ####
network_dir=networks

#### Regulatory network ####
reg_net=regulatory.network

#### Gencode file path ####
gencode=gencode

#### Reference genome sequence ####
reference_file=reference_genome.fa
 
#### Ancestral genome sequence ####
ancestral_file=human_ancestor_GRCh37_e59.fa

#### Gene list path ####
gene_info_dir=gene_lists

#### Recurrence database ####
cancer_dir=cancer_recurrence

#### Gene selection file ####
selection=GENE.strong_selection.txt

#### Weighted scoring scheme ####
weight_file=weighted.score.txt