HiCdat: a fast and easy-to-use Hi-C data analysis tool
HiCdat: a fast and easy-to-use Hi-C data analysis tool
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DOI：
10.1186/s12859-015-0678-x
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发表时间：
2015-09-03
影响因子：
3
通讯作者：
Grossniklaus, Ueli
中科院分区：
文献类型：
--
作者：
Schmid, Marc W.;Grob, Stefan;Grossniklaus, Ueli
背景：利用染色体构象捕获（3C）技术研究核结构是生物学的一个新前沿。随着测序成本的进一步降低，Hi-C将核结构描述为表型的潜力即将展现。使用Hi-C不同的细胞类型，条件或遗传背景之间的表型比较，Hi-C数据处理需要更容易访问biologist.Results：HiCdat提供了一个简单的图形用户界面的数据预处理和更高层次的数据分析工具的集合在R。数据预处理还支持Hi-C数据深入分析所需的各种额外数据类型（例如RNA-Seq、ChIP-Seq和BS-Seq）。结论：HiCdat易于使用，提供从比对读段到深入分析的解决方案。重要的是，HiCdat专注于分析染色体的较大结构特征，它们与基因组和表观基因组特征的相关性，以及比较研究。它使用简单的输入和输出格式，因此可以很容易地集成到现有的工作流程中或与替代工具相结合。
Background: The 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.Results: HiCdat 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).Conclusions: HiCdat 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.