HiChIP-Peaks: A HiChIP peak calling algorithm
HiChIP-Peaks: A HiChIP peak calling algorithm
复制标题
HiChIP-Peaks：HiChIP 峰值检出算法
DOI：
10.1101/682781
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发表时间：
2019
期刊：
影响因子：
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通讯作者：
Shi C
中科院分区：
文献类型：
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作者：
Shi C
动机hichip是一个强大的工具来询问三维染色质组织。目前使用HiChIP数据分析染色质环机制的工具需要识别环锚点才能正常工作。然而，目前从HiChIP数据中发现这些锚点的方法并不令人满意，要么有很高的错误发现率，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本的峰值进行定量比较，无法充分利用来自HiChIP数据集的可用信息。我们开发了一种基于以再连接位点为中心的HiChIP数据表示的新工具，以识别HiChIP数据集中的峰值，随后可用于其他工具以发现环路。这增加了这些工具的可靠性，并在测序深度降低时提高了召回率。我们还提供了一种方法来计数读取映射到不同样本的峰值，该方法可用于使用HiChIP数据进行差分峰分析。可用性和实施hichip - peaks可在https://github.com/ChenfuShi/HiChIP_peaks.Supplementary上免费获得。补充数据可在bioinformatics online上获得。
MotivationHiChIP 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.ResultsWe 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 and implementationHiChIP-Peaks is freely available at https://github.com/ChenfuShi/HiChIP_peaks.Supplementary informationSupplementary data are available atBioinformaticsonline.