Table 1

Peak-calling algorithms for ChIP-seq

Name of algorithm

Notable features


MACS [23]

Uses both a control library and local statistics to minimize bias

SICER [14]

Designed for detecting diffusely enriched regions; for example, histone modification

PeakSeq [24]

Corrects for reference genome mappability and local statistics

SISSRs [25]

High resolution, precise identification of binding-site location

F-seq [26]

Uses kernel density estimation


Liu et al. BMC Biology 2010 8:56   doi:10.1186/1741-7007-8-56

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