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. Author manuscript; available in PMC: 2018 Jan 11.
Published in final edited form as: Nat Rev Mol Cell Biol. 2016 Sep 1;17(12):743–755. doi: 10.1038/nrm.2016.104

Table 5.

Approaches for chromatin contact peak-calling

Approach Assumption on background model Pros Cons Refs
Jin et al. Global background Models contact-frequency uncertainty as a negative binomial distribution Variability of local chromatin organization may introduce biases 19
Fit-Hi-C Global background Accurate background model using non-parametric spline Variability of local chromatin organization may introduce biases 91
GOTHiC Global background Models contact-frequency uncertainty as binomial distribution Variability of local chromatin organization may introduce biases 54
HiCCUPS Local background Designed for high-resolution Hi-C data Deep sequencing is required 27
HMRF Global or local background Models spatial dependency among adjacent, interacting loci High computation cost 93

GOTHiC, genome organisation through HiC; HiCCUPS, Hi-C computational unbiased peak search; HMRF, hidden Markov random field.