Motivation

HiChIP is a powerful tool to interrogate 3D chromatin organization. Current tools to analyse chromatin looping mechanisms using HiChIP data require the identification of loop anchors to work properly. However, current approaches to discover these anchors from HiChIP data are not satisfactory, having either a very high false discovery rate or strong dependence on sequencing depth. Moreover, these tools do not allow quantitative comparison of peaks across different samples, failing to fully exploit the information available from HiChIP datasets.

Results

We develop a new tool based on a representation of HiChIP data centred on the re-ligation sites to identify peaks from HiChIP datasets, which can subsequently be used in other tools for loop discovery. This increases the reliability of these tools and improves recall rate as sequencing depth is reduced. We also provide a method to count reads mapping to peaks across samples, which can be used for differential peak analysis using HiChIP data.

Availability

HiChIP-Peaks is freely available at https://github.com/ChenfuShi/HiChIP_peaks

Supplementary information

Supplementary dataSupplementary data are available at Bioinformatics online.

中文翻译：

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HiChIP-Peaks：HiChIP 峰值调用算法。

动机

HiChIP 是一个强大的工具来询问 3D 染色质组织。当前使用 HiChIP 数据分析染色质循环机制的工具需要识别循环锚才能正常工作。然而，目前从 HiChIP 数据中发现这些锚点的方法并不令人满意，要么错误发现率非常高，要么对测序深度有很强的依赖性。此外，这些工具不允许对不同样品的峰进行定量比较，未能充分利用 HiChIP 数据集中的可用信息。

结果

我们基于以重新连接位点为中心的 HiChIP 数据表示开发了一种新工具，以识别 HiChIP 数据集中的峰，随后可用于其他工具以进行循环发现。这增加了这些工具的可靠性，并随着测序深度的降低而提高召回率。我们还提供了一种方法来计算映射到跨样本峰的读数，该方法可用于使用 HiChIP 数据进行差异峰分析。

可用性

HiChIP-Peaks 可在 https://github.com/ChenfuShi/HiChIP_peaks 免费获得

补充资料

补充数据补充数据可在生物信息学在线获得。