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Methods in molecular biology (Clifton, N.J.)
2023;2624 1-6.

DNA Methylation Data Analysis Using Msuite.

Xiaojian Liu, Pengxiang Yuan, Kun Sun
Author Information
  1. Xiaojian Liu: Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China.
  2. Pengxiang Yuan: Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China.
  3. Kun Sun: Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China. sunkun@szbl.ac.cn.
PMID: 36723805 DOI: 10.1007/978-1-0716-2962-8_1

Abstract

DNA methylation is a widespread epigenetic modification responsible for many biological regulation pathways. The development of various powerful biochemical assays, including conventional bisulfite treatment-based and emerging bisulfite-free techniques, has promised high-resolution DNA methylome profiling and significantly propelled the DNA methylation research field. However, the analysis of large-scale data generated from such assays is still complex and challenging. In this paper, we present a step-by-step protocol for using Msuite for whole-spectrum DNA methylation data analysis, from quality control, read alignment, to methylation call and data visualization. The Msuite package and a testing dataset are freely available at https://github.com/hellosunking/Msuite.

Keywords

Bisulfite sequencing CpG dinucleotides Data visualization

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MeSH Term

DNA Methylation
Epigenesis, Genetic
Data Analysis
Sequence Analysis, DNA
Sulfites
CpG Islands
Software

Chemicals

Sulfites
Journal Article

Word Cloud

Created with Highcharts 10.0.0DNAmethylationdataMsuiteassaysanalysisvisualizationDatawidespreadepigeneticmodificationresponsiblemanybiologicalregulationpathwaysdevelopmentvariouspowerfulbiochemicalincludingconventionalbisulfitetreatment-basedemergingbisulfite-freetechniquespromisedhigh-resolutionmethylomeprofilingsignificantlypropelledresearchfieldHoweverlarge-scalegeneratedstillcomplexchallengingpaperpresentstep-by-stepprotocolusingwhole-spectrumqualitycontrolreadalignmentcallpackagetestingdatasetfreelyavailablehttps://githubcom/hellosunking/MsuiteMethylationAnalysisUsingBisulfitesequencingCpGdinucleotides

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