Table 1 Peak-calling algorithms for ChIP-seq
From: Q&A: ChIP-seq technologies and the study of gene regulation
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 |