Table 1.

Comparison between SCAN-ATAC Sim and previous methods and a brief list of parameters that control the simulation

Features	Direct down sampling	Peak region sampling	SCAN-ATAC Sim
Read-level simulation	Yes	No	Yes
Flexible signal-to-noise	No	No	Yes
Diploid genomic constraint	No	Yes	Yes
Short runtime	No	No	Yes
Long flag	Default value	Long flag	Default value
–cell_number	10 000	–min_frag	1000
–signal_to_noise	0.7	–max_frag	20 000
–frag_num	3000	–extend_peak_size	1000
–variance	0.5	–bin_size	1000