NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data

BMC Genomics

Table 1 Summary of programs used for comparison

	Profile	Strand specific	Statistical model	Peak criteria	Rank by	Ref
HPeak	Sliding window	Indirect	Hidden Markov model	Tag counts	Tag counts	[10]
WTD	Sliding window	Direct		Score	P-value	[11]
MTC	Sliding window	Direct		Score	P-value	[11]
CisGenome	Sliding window	Indirect	Binomial	Tag counts	Tag counts	[9]
MACS	Sliding window	Indirect	Local Poisson	P-value	P-value	[8]
QuEST	Gaussian kernel density	Indirect	Poisson	Height threshold	Q-value	[13]
SISSRs	Sliding window	Direct		Tag counts with sign change	P-value	[12]
NEXT-peak	NEXT-peak kernel density	Direct	Poisson per base pair	Likelihood	Estimated binding intensity (2ν)

ISSN: 1471-2164