Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.

ABSTRACT: Capture Hi-C is widely used to obtain high-resolution profiles of chromosomal interactions involving, at least on one end, regions of interest such as gene promoters. Signal detection in Capture Hi-C data is challenging and cannot be adequately accomplished with tools developed for other chromosome conformation capture methods, including standard Hi-C. Capture Hi-C Analysis of Genomic Organization (CHiCAGO) is a computational pipeline developed specifically for Capture Hi-C analysis. It implements a statistical model accounting for biological and technical background components, as well as bespoke normalization and multiple testing procedures for this data type. Here we provide a step-by-step guide to the CHiCAGO workflow that is aimed at users with basic experience of the command line and

SUBMITTER: Freire-Pritchett P 

PROVIDER: S-EPMC7612634 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature