Table 5. Optimization of peakcalling with Peakranger.

Number of peaks identified for each condition. ChIPmentation on top. In bold: 1000 bp was selected as the best extension length and applied to N-ChIP data below. N-ChIP A is for 0.8x10 ⁶ cells.

Sample	C1			C3			C5			C7
cell equivalents	1,000,000			10,000			1,000			100
	ChIPmentation			ChIPmentation			ChIPmentation			ChIPmentation
Peakranger read extension length in bp	L1	R1	N-ChIP A	L3	R3	N-ChIP B	L5	R5	N-ChIP C	L7	R7
100	6,871	6,767		625	424		200	370		4,732	5,683
300	10,369	9,545		2,125	1,211		499	635		3,944	5,264
600	10,581	9,924		3,513	2,823		610	813		3,197	3,816
1,000	9,632	9,835	8,320	4,033	2,749	3,888	695	811	131	3,098	3,416
1,500	9,901	9,426		3,315	2,925		847	837		4,019	3,526
2,000	9,067	8,353		3,052	2,631		626	693		4,336	3,897