Statistically rigorous and computationally efficient chromatin stripe detection with Quagga.

ABSTRACT: Chromatin stripes are architectural chromatin features in which a singular loop anchor interacts with a contiguous region of DNA so, at the bulk sequencing level, it appears as a long stripe on chromatin contact matrices. Stripes are thought to play an important role in gene regulation and have been implicated in regulating a cell's lineage determination. Therefore, integrated analysis of stripes with genomic and epigenomic features at a genome-wide scale shows vast potential in understanding the cooperation between regulatory elements in 3D nucleome. To this end, we present Quagga, a computational tool for detection and statistical verification of genomic architectural stripes from Hi-C or Micro-C chromatin contact maps, that relies on robust image processing techniques and rigorous stati

SUBMITTER: Feng F 

PROVIDER: S-EPMC12758393 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature