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首页> 外文期刊>BMC Genomics >MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data
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MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data

机译：MethGo：用于分析全基因组亚硫酸氢盐测序数据的综合工具

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Background DNA methylation is a major epigenetic modification regulating several biological processes. A standard approach to measure DNA methylation is bisulfite sequencing (BS-Seq). BS-Seq couples bisulfite conversion of DNA with next-generation sequencing to profile genome-wide DNA methylation at single base resolution. The analysis of BS-Seq data involves the use of customized aligners for mapping bisulfite converted reads and the bioinformatic pipelines for downstream data analysis. Results Here we developed MethGo, a software tool designed for the analysis of data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS). MethGo provides both genomic and epigenomic analyses including: 1) coverage distribution of each cytosine; 2) global cytosine methylation level; 3) cytosine methylation level distribution; 4) cytosine methylation level of genomic elements; 5) chromosome-wide cytosine methylation level distribution; 6) Gene-centric cytosine methylation level; 7) cytosine methylation levels at transcription factor binding sites (TFBSs); 8) single nucleotide polymorphism (SNP) calling, and 9) copy number variation (CNV) calling. Conclusions MethGo is a simple and effective tool for the analysis of BS-Seq data including both WGBS and RRBS. It contains 9 analyses in 5 major modules to profile (epi)genome. It profiles genome-wide DNA methylation in global and in gene level scale. It can also analyze the methylation pattern around the transcription factor binding sites, and assess genetic variations such as SNPs and CNVs. MethGo is coded in Python and is publically available at http://paoyangchen-laboratory.github.io/methgo/ .
机译：背景DNA甲基化是调节几种生物学过程的主要表观遗传修饰。测量DNA甲基化的标准方法是亚硫酸氢盐测序（BS-Seq）。 BS-Seq将DNA的亚硫酸氢盐转化与下一代测序结合在一起，以单碱基分辨率分析全基因组DNA甲基化。 BS-Seq数据的分析涉及使用定制的比对器来绘制亚硫酸氢盐转换的读图，并使用生物信息学管道进行下游数据分析。结果我们在这里开发了MethGo，这是一种软件工具，用于分析全基因组亚硫酸氢盐测序（WGBS）和简化表示亚硫酸氢盐测序（RRBS）的数据。 MethGo提供了基因组和表观基因组分析，包括：1）每个胞嘧啶的覆盖范围分布; 2）总胞嘧啶甲基化水平; 3）胞嘧啶甲基化水平分布; 4）基因组元件胞嘧啶甲基化水平; 5）全染色体胞嘧啶甲基化水平分布; 6）以基因为中心的胞嘧啶甲基化水平; 7）转录因子结合位点（TFBS）的胞嘧啶甲基化水平; 8）单核苷酸多态性（SNP）调用，以及9）拷贝数变异（CNV）调用。结论MethGo是分析BS-Seq数据（包括WGBS和RRBS）的简单有效的工具。它包含5个主要模块的9个分析，以分析（epi）基因组。它概述了全球和基因水平规模的全基因组DNA甲基化。它还可以分析转录因子结合位点周围的甲基化模式，并评估SNP和CNV等遗传变异。 MethGo用Python编码，可以在http://paoyangchen-laboratory.github.io/methgo/上公开获得。

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