Raineri Emanuele, Alberola I Pla Mariona, Dabad Marc, Heath Simon
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.
Bioinform Adv. 2023 Jan 23;3(1):vbac101. doi: 10.1093/bioadv/vbac101. eCollection 2023.
Nanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here, we exploit this property to search for regions where one can define subpopulations of molecules based on methylation patterns. As an example, we run our clustering algorithm on known imprinted genes; we also scan chromosome 15 looking for windows corresponding to heterogeneous methylation. Our software can also compute the covariance of methylation across these regions while keeping into account the mixture of different types of reads.
https://github.com/EmanueleRaineri/cvlr.
Supplementary data are available at online.
纳米孔测序读数编码了CpG二核苷酸中胞嘧啶甲基化状态的信息。读数的长度使得查看由多个位点组成的模式相对容易；在这里，我们利用这一特性来搜索可以根据甲基化模式定义分子亚群的区域。作为一个例子，我们在已知的印记基因上运行聚类算法；我们还扫描15号染色体以寻找与异质甲基化相对应的窗口。我们的软件还可以计算这些区域甲基化的协方差，同时考虑不同类型读数的混合情况。
https://github.com/EmanueleRaineri/cvlr。
补充数据可在网上获取。
