Argument	Synopsis (* = required)	Detail
--t	*Treatment BED file	Type 1 ssDNA BED file
--c	*Control BED file	Type 1 ssDNA BED file
--gSz	*Effective genome size	Estimated size of mappable genome
--gName	*Genome/species name	Use pre-computed effective genome size
	(can be used instead of --gSz)	For human: hg19 | hg38 | hg | hs | human For mouse: mm9 | mm10 | mm | mouse For rat: rn | rat
--name	*Name prefix for output files	-
--out	Output folder	Default = current folder
--blist	Blacklist file	BED file of genomic regions with sequencing biases that result in spurious peak calls i.e. for mouse (mm10 genome): $CHSPATH/mm10_hotspot_blacklist.bed
--tuniq	Treatment BED file with ONLY unique fragments	Optional, but not recommended
--cuniq	Control BED file with ONLY unique fragments	Optional, but not recommended
--debug	DEBUG mode	Builds scripts but does not execute. Note: This is a logical argument, so does not take any value (pass as --debug)
--q30	Q30 mode	Use only fragments where both reads have a q-score >= 30. This is useful for removing reads that map with low confidence (i.e. to high copy repeats). Note: This is a logical argument, so does not take any value (pass as --q30)
--nc	Do not call peaks	Do not run peak calling. Note: This is a logical argument, so does not take any value (pass as --debug)
--h/help	Show help