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

BMC Genomics

Table 1 Preprocessing: IMUB reads and runtime

Factor	Dataset	Reads	IMUB originally	IMUB Q-nexus	Runtime (m)
Dorsal	SRR1175698	18,983,666	6,404,431	6,234,888	6
	SRR1175699	21,926,113	6,219,935	6,054,824	6
Max	SRR1175700	30,781,699	11,100,441	11,381,661	10
	SRR1509031	33,125,449	7,557,857	7,517,583	9
Myc	SRR1175701	27,404,713	3,714,258	4,724,027	6
	SRR1509032	31,044,447	7,366,642	7,480,050	8
Twist	SRR1509029	34,042,864	14,146,225	14,455,901	12
	SRR1509030	92,712,131	30,370,792	30,565,366	31
TBP	SRR1175702	52,656,846	12,924,627	13,349,578	19
	SRR1175703	206,910,978	8,978,714	9,164,510	57

We compared the numbers of IMUB reads of the original analysis [11] and Q-nexus preprocessing. By and large, comparable numbers of reads are mapped. The calculations were performed using four threads on a desktop computer with an Intel Core i7-3770 (3.4GHz). On average, the Q-nexus preprocessing can be performed in less than 17 minutes

ISSN: 1471-2164