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 (fourSig, FourCSeq, 4C-ker and w4Cseq) 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 Arabidopsis thaliana by the FLOWERING LOCUS C (FLC) gene and to long-range chromatin interactions in mouse embryonic stem cells.

中文翻译：

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4C-seq 数据分析：方法比较

环形染色体构象捕获技术随后进行测序 (4C-seq) 已被用于许多研究以研究 DNA 片段之间的染色体相互作用。计算管道已经开发和发布，提供了 4C-seq 数据处理和统计分析的各种可能性。在这里，我们概述了四个这样的管道（fourSig、FourCSeq、4C-ker 和 w4Cseq），并考虑了最重要的计算阶段。我们提供了这些方法的比较，并讨论了它们的优点和可能的弱点。我们使用从两个不同物种获得的数据来说明结果，该研究致力于通过开花基因座 C (FLC) 基因对拟南芥的春化控制和小鼠胚胎干细胞中的长程染色质相互作用进行研究。