Luu Phuc-Loi, Ong Phuc-Thinh, Loc Tran Thai Huu, Lam Dilys, Pidsley Ruth, Stirzaker Clare, Clark Susan J
Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia.
Bioinformatics. 2021 Aug 9;37(15):2198-2200. doi: 10.1093/bioinformatics/btaa1060.
DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of an epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualization and remotely sharing data with collaborators and clinicians.
MethPanel is freely available at https://github.com/thinhong/MethPanel.
Supplementary data are available at Bioinformatics online.
细胞中的DNA甲基化模式与基因表达及细胞表型相关，包括疾病状态。亚硫酸氢盐PCR测序常用于评估不同细胞间基因组区域的甲基化谱。在此，我们开发了MethPanel，这是一个带有交互式图形界面的计算流程，用于快速分析多重亚硫酸氢盐PCR测序数据。MethPanel包含从基因组比对到DNA甲基化调用的完整分析工作流程，并支持无限数量的PCR扩增子和输入样本。MethPanel具有重要且独特的功能，如计算表观多态性得分和亚硫酸氢盐PCR偏差校正能力，其设计使得所有样本的甲基化数据能够并行处理。输出结果会自动转发到一个shinyApp，以便于显示、可视化以及与合作者和临床医生远程共享数据。
MethPanel可在https://github.com/thinhong/MethPanel上免费获取。
补充数据可在《生物信息学》在线获取。
