# --effectiveGenomeSize The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. Also, if repetitive regions were not included in the mapping of
# reads, the effective genome size needs to be adjusted accordingly.
EFFECTIVEGENOMESIZE:'820000000'#source = http://plant-plasticity.github.io/resources/3_ATAC-seq%20data%20processing.pdf #option is --effectiveGenomeSize
EXTENDREADS:'200'# extend each reads with a 200bp to match the average fragment size of the ChIP experiment
binSize:"1000"
ignoreForNormalization:"SL3.0ch00"#list here space-delimited chromosomes that should be ignored for normalization, sex chromosomes usually.
smoothLength:"40"
normalizeUsing:"RPKM"
bamcompare:
binSize:"1000"
normalizeUsing:"RPKM"#others choices are CPM, BPM, RPGC, None more documentation:https://deeptools.readthedocs.io/en/develop/content/tools/bamCompare.html?highlight=bamcompare
EFFECTIVEGENOMESIZE:'820000000'
operation :"log2"#others choices are ratio, subtract, add, mean, reciprocal_ratio, first, second more documentation:https://deeptools.readthedocs.io/en/develop/content/tools/bamCompare.html?highlight=bamcompare
smoothLength:"40"
scaleFactorsMethod:"None"#others choices are readCount, ,SES
ignoreForNormalization:"SL3.0ch00"#list here space-delimited chromosomes that should be ignored for normalization, sex chromosomes usually.
# macs2 Parameters:
# for information over macs2, refer to https://github.com/taoliu/MACS