An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.

ABSTRACT:

Background

DNA methylation plays crucial roles in most eukaryotic organisms. Bisulfite sequencing (BS-Seq) is a sequencing approach that provides quantitative cytosine methylation levels in genome-wide scope and single-base resolution. However, genomic variations such as insertions and deletions (indels) affect methylation calling, and the alignment of reads near/across indels becomes inaccurate in the presence of polymorphisms. Hence, the simultaneous detection of DNA methylation and indels is important for exploring the mechanisms of functional regulation in organisms.

Results

These problems motivated us to develop the algorithm BatMeth2, which can align BS reads with high accuracy while allowing for variable-length indels with respect to the reference genome. The results

SUBMITTER: Zhou Q 

PROVIDER: S-EPMC6343306 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature