CASPIAN: A method to identify chromatin topological associated domains based on spatial density cluster.

ABSTRACT: With the development of Hi-C technology, the detection of topologically associated domains (TADs) boundaries plays an important role in exploring the relationship between gene structure and expression. However, a method that can identify accurate TAD boundaries from the Hi-C contact matrix with different resolutions is currently lacking. We proposed a method named CASPIAN that can identify chromatin TAD boundaries based on the spatial density clustering algorithm. CASPIAN requires few parameters to call TADs. This method is realized using the hierarchical density-based clustering method HDBSCAN, where the distance of pairwise bins is calculated based on three distance metrics (Euclidean, Manhattan, and Chebyshev distance metric) to adapt to the characteristics of the Hi-C contact matrix ge

SUBMITTER: Gong H 

PROVIDER: S-EPMC9464881 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature