Loop detection using Hi-C data with HiCExplorer.

ABSTRACT:

Background

Chromatin loops are an essential factor in the structural organization of the genome; however, their detection in Hi-C interaction matrices is a challenging and compute-intensive task. The approach presented here, integrated into the HiCExplorer software, shows a chromatin loop detection algorithm that applies a strict candidate selection based on continuous negative binomial distributions and performs a Wilcoxon rank-sum test to detect enriched Hi-C interactions.

Results

HiCExplorer's loop detection has a high detection rate and accuracy. It is the fastest available CPU implementation and utilizes all threads offered by modern multicore platforms.

Conclusions

HiCExplorer's method to detect loops by using a continuous negative binomial function combined wit

SUBMITTER: Wolff J 

PROVIDER: S-EPMC9270730 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature