Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

BMC Genomics

Table 3 Evaluation of binding characteristics

Factor	Dataset	5’ end coverage	Cross-correlation	MACS2	MACE	Q-nexus
Dorsal	SRR1175698	18	42	28	47	18
	SRR1175699	18	42	28	62	18
Max	SRR1175700	10	42	19	41	10
	SRR1509031	10	42	32	46	12
Myc	SRR1175701	NA	42	29	42	9
	SRR1509032	NA	42	32	38	12
Twist	SRR1509029	11	42	24	39	12
	SRR1509030	11	42	21	38	12
TBP	SRR1175702	NA	42	37	41	12
	SRR1175703	NA	42	39	42	12

Protected-region width estimates from 5’ coverage around motif centered binding sites, cross-correlation plot, MACS2, MACE (optimal border pair size), and the width of the protected region estimated by Q-nexus. The estimates derived by Q-nexus are consistent with those derived by the method of 5’ coverage around motif centered binding sites

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