Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 61-479 Poznań, Poland.
Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands.
J Bioinform Comput Biol. 2020 Feb;18(1):2050001. doi: 10.1142/S0219720020500018.
The circular chromosome conformation capture technique followed by sequencing (4C-seq) has been used in a number of studies to investigate chromosomal interactions between DNA fragments. Computational pipelines have been developed and published that offer various possibilities of 4C-seq data processing and statistical analysis. Here, we present an overview of four of such pipelines (, , and ) taking into account the most important stages of computations. We provide comparisons of the methods and discuss their advantages and possible weaknesses. We illustrate the results with the use of data obtained for two different species, in a study devoted to vernalization control in by the () gene and to long-range chromatin interactions in mouse embryonic stem cells.
环状染色体构象捕获技术结合测序（4C-seq）已在多项研究中用于研究 DNA 片段之间的染色体相互作用。已经开发并发布了计算管道，提供了 4C-seq 数据处理和统计分析的各种可能性。在这里，我们考虑到计算的最重要阶段，概述了其中的四个管道（,, 和 ）。我们比较了这些方法，并讨论了它们的优点和可能的弱点。我们使用在两个不同物种中获得的数据来说明结果，该研究致力于通过 ()基因控制春化以及在小鼠胚胎干细胞中的长距离染色质相互作用。
