config_finding-ORIs.txt

read_directory=aligned_reads_SNScontrol_Tb427-2018-55_bowtie2               
# path to aligned reads

output_dir=StrandSpecific_norrowPeaks_RNASE_p05_Tb427-2018_p005_mergedBSF
# output directory name (generated by the script in the working directory)

file_prefix=aln-pe_TB_trimmed_unique_sorted_reheadered_dups-removed                 
# prefix of mapped reads ($sample$prefix.bam)

input_list=("15-17-19")      
# sample name as found in bam files 

overlap_list=(50)                                                  
# peak overlap to be excluded

window_list=(500)                                       
# window size for peak pair selection