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.

SUBMITTER: Sun S 

PROVIDER: S-EPMC3765750 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature