title: MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data.
abstract: 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/.
authors.forename: Wen-Wei
authors.initials: WW
authors.lastname: Liao
authors.forename: Ming-Ren
authors.initials: MR
authors.lastname: Yen
authors.forename: Evaline
authors.initials: E
authors.lastname: Ju
authors.forename: Fei-Man
authors.initials: FM
authors.lastname: Hsu
authors.forename: Larry
authors.initials: L
authors.lastname: Lam
authors.forename: Pao-Yang
authors.initials: PY
authors.lastname: Chen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D014644:Genetic Variation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites; D014157:Transcription Factors / Q000235:genetics
chemical_list: D013447:Sulfites; D014157:Transcription Factors; C042345:hydrogen sulfite