ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.
Fiche publication
Date publication
mai 2019
Journal
Genome biology
Auteurs
Membres identifiés du Cancéropôle Est :
Dr SEXTON Thomas
Tous les auteurs :
Ben Zouari Y, Molitor AM, Sikorska N, Pancaldi V, Sexton T
Lien Pubmed
Résumé
Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks.
Mots clés
Biological replicates, Capture Hi-C, Chromatin assortativity, Chromatin loops, Gene regulation, Promoter-enhancer interactions
Référence
Genome Biol.. 2019 May 22;20(1):102