title: MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment.
abstract: BACKGROUND
  DNA methylation is an epigenetic event that adds a methyl-group to the 5' cytosine. This epigenetic modification can significantly affect gene expression in both normal and diseased cells. Hence, it is important to study methylation signals at the single cytosine site level, which is now possible utilizing bisulfite conversion technique (i.e., converting unmethylated Cs to Us and then to Ts after PCR amplification) and next generation sequencing (NGS) technologies. Despite the advances of NGS technologies, certain quality issues remain. Some of the more prevalent quality issues involve low per-base sequencing quality at the 3' end, PCR amplification bias, and bisulfite conversion rates. Therefore, it is important to conduct quality assessment before downstream analysis. To the best of our knowledge, no existing software packages can generally assess the quality of methylation sequencing data generated based on different bisulfite-treated protocols.
  
  
  RESULTS
  To conduct the quality assessment of bisulfite methylation sequencing data, we have developed a pipeline named MethyQA. MethyQA combines currently available open-source software packages with our own custom programs written in Perl and R. The pipeline can provide quality assessment results for tens of millions of reads in under an hour. The novelty of our pipeline lies in its examination of bisulfite conversion rates and of the DNA sequence structure of regions that have different conversion rates or coverage.
  
  
  CONCLUSIONS
  MethyQA is a new software package that provides users with a unique insight into the methylation sequencing data they are researching. It allows the users to determine the quality of their data and better prepares them to address the research questions that lie ahead. Due to the speed and efficiency at which MethyQA operates, it will become an important tool for studies dealing with bisulfite methylation sequencing data.
authors: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland 44106, Ohio, USA. ssun5211@yahoo.com.
authors: Shuying
authors: S
authors: Sun
authors: Aaron
authors: A
authors: Noviski
authors: Xiaoqing
authors: X
authors: Yu
mesh_terms: D004247:DNA / Q000032:analysis / Q000737:chemistry* / Q000235:genetics; D019175:DNA Methylation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites / Q000032:analysis / Q000737:chemistry / Q000378:metabolism
chemical_list: D013447:Sulfites; D004247:DNA; C042345:hydrogen sulfite
references: BMC Bioinformatics. 2009 Jul 27;10:232
references: 19635165
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8681-6
references: 10411935
references: Cancer Res. 2006 Jan 1;66(1):29-33
references: 16397211
references: Nat Protoc. 2011 Apr;6(4):468-81
references: 21412275
references: Nature. 2008 Mar 13;452(7184):215-9
references: 18278030
references: Bioinformatics. 2011 Jun 1;27(11):1571-2
references: 21493656
references: Nat Genet. 2011 Jun 26;43(8):768-75
references: 21706001
references: Cancer Res. 2001 Apr 15;61(8):3225-9
references: 11309270
references: BioData Min. 2012 Jun 18;5(1):6
references: 22709551
references: Int J Cancer. 2010 Jan 15;126(2):474-82
references: 19618401
references: BMC Bioinformatics. 2010 Apr 23;11:203
references: 20416082
references: J Pathol. 2007 May;212(1):83-90
references: 17334979
references: Ann N Y Acad Sci. 2003 Mar;983:243-50
references: 12724229
references: PLoS One. 2008 Apr 30;3(4):e2079
references: 18446232
references: Nature. 2008 Aug 7;454(7205):766-70
references: 18600261
references: Cell. 2008 May 2;133(3):523-36
references: 18423832
references: Bioinformatics. 2012 Jul 1;28(13):1795-6
references: 22563065
references: Bioinformatics. 2012 Aug 15;28(16):2180-1
references: 22689387
references: Carcinogenesis. 2002 Feb;23(2):231-6
references: 11872627
references: Bioinformatics. 2010 Feb 15;26(4):572-3
references: 20031974
references: Ann Oncol. 2011 Jan;22(1):24-29
references: 20591821
references: Expert Rev Mol Med. 2002 Mar 04;4(4):1-17
references: 14987388
references: Nature. 2009 Nov 19;462(7271):315-22
references: 19829295
references: Bioinformatics. 2010 Apr 1;26(7):873-81
references: 20147302
references: Hum Mol Genet. 1999 Mar;8(3):459-70
references: 9949205
references: Dis Markers. 2007;23(1-2):51-71
references: 17325426
references: Oncogene. 2002 Aug 12;21(35):5462-82
references: 12154408
references: Clin Cancer Res. 2006 Dec 15;12(24):7205-8
references: 17189390
references: Nature. 2011 Mar 3;471(7336):68-73
references: 21289626
references: Cancer Metastasis Rev. 2010 Mar;29(1):181-206
references: 20135198
references: Endocr Relat Cancer. 2001 Jun;8(2):115-27
references: 11446343
references: PLoS One. 2011 Feb 25;6(2):e17490
references: 21364760
references: Bioinformatics. 2011 Sep 1;27(17):2435-6
references: 21724594
references: Nat Methods. 2010 Jun;7(6):435-7
references: 20508637
references: Clin Cancer Res. 2000 Apr;6(4):1432-8
references: 10778974
references: Cancer Inform. 2007 Feb 07;3:43-54
references: 19455234
references: Genome Res. 2009 Jun;19(6):1044-56
references: 19273619
references: Cancer Res. 2008 Dec 15;68(24):10257-66
references: 19074894
references: BMC Bioinformatics. 2011 Feb 15;12:54
references: 21324121