Table 1.

Description of 8 approaches used to calculate ATAC-seq differential accessibility

#	Genomic regions	Tool	Normalization	DA testing
I	MACS2 [27]	DiffBind [29]	Full library size	DESeq2 [31]
II	MACS2 [27]	DiffBind [29]	Reads in peaks	DESeq2 [31]
III	MACS2 [27]	csaw [28]	TMM [34]	edgeR [30]
IV	MACS2 [27]	csaw [28]	Loess	edgeR [30]
V	csaw [28]	csaw [28]	TMM [34]	edgeR [30]
VI	csaw [28]	csaw [28]	Loess	edgeR [30]
VII	MACS2 [27]	csaw [28] | voom [32]	Log2cpm	limma [33]
VIII	MACS2 [27]	csaw [28] | voom [32]	Quantile [35]	limma [33]