Skip to main content
eScholarship
Open Access Publications from the University of California

UC Riverside

UC Riverside Previously Published Works bannerUC Riverside

Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Abstract

We present M ustache , a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. M ustache employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in a multi-scale representation of chromatin contact maps parametrized by the size of the smoothing kernel. When applied to high-resolution Hi-C and Micro-C data, M ustache detects loops at a wide range of genomic distances, identifying potential structural and regulatory interactions that are supported by independent conformation capture experiments as well as by known correlates of loop formation such as CTCF binding, enhancers and promoters. Unlike the commonly used HiCCUPS tool, M ustache runs on general-purpose CPUs and it is very time efficient with a runtime of only a few minutes per chromosome for 5kb-resolution human genome contact maps. Extensive experimental results show that M ustache reports two to three times the number of HiCCUPS loops, which are reproducible across replicates. It also recovers a larger proportion of published ChIA-PET and HiChIP loops than HiCCUPS. A comparative analysis of M ustache ’s experimental results on Hi-C and Micro-C data confirms strong agreement between the two datasets with Micro-C providing better power for loop detection. Overall, our experimental results show that M ustache enables a more efficient and comprehensive analysis of the chromatin looping from high-resolution Hi-C and Micro-C datasets. M ustache is freely available at https://github.com/ay-lab/mustache .

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
For improved accessibility of PDF content, download the file to your device.
Current View