HiCdat: a fast and easy-to-use Hi-C data analysis tool

BMC Bioinformatics

Software

Ueli Grossniklaus¹  Stefan Grob¹  Marc W. Schmid¹ 

[1] Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zürich, Switzerland;Zurich-Basel Plant Science Center, Universitätstrasse 2, 8092, Zürich, Switzerland;

关键词: Chromosome Conformation Capture (3C);    Nuclear architecture;    Hi-C;    Data analysis;    Sample comparison;    Structural domains;    Correlation to (epi-)genome;   

DOI  :  10.1186/s12859-015-0678-x

 received in 2015-01-28, accepted in 2015-07-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists.ResultsHiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq).ConclusionsHiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

【 授权许可】

CC BY   
© Schmid et al. 2015