ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C

Genome Biology

Anne M. Molitor¹  Tom Sexton¹  Natalia Sikorska¹  Yousra Ben Zouari¹  Vera Pancaldi² 

[1] 0000 0004 0638 2716, grid.420255.4, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France;0000 0004 0638 2716, grid.420255.4, CNRS UMR7104, Illkirch, France;INSERM U1258, Illkirch, France;0000 0001 2157 9291, grid.11843.3f, University of Strasbourg, Illkirch, France;grid.468186.5, Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM U1037, Toulouse, France;0000 0001 0723 035X, grid.15781.3a, University Paul Sabatier III, Toulouse, France;0000 0004 0387 1602, grid.10097.3f, Barcelona Supercomputing Center, Barcelona, Spain;

关键词: Promoter-enhancer interactions;    Chromatin loops;    Capture Hi-C;    Biological replicates;    Gene regulation;    Chromatin assortativity;   

DOI  :  10.1186/s13059-019-1706-3

来源: publisher

【 摘 要 】

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.

【 授权许可】

CC BY