期刊
BRIEFINGS IN BIOINFORMATICS
卷 16, 期 3, 页码 369-379出版社
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbu016
关键词
DNA methylation; epigenetics; high-throughput sequencing; bisulfite sequencing
资金
- National Research Foundation
- Singapore Ministry of Education under its Centres of Excellence initiative
- National Medical Research Council (Singapore) [NMRC/IRG/1278/2010]
The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation beyond CpG sites and CpG islands. These technologies have opened new avenues to understand the interplay between epigenetic events, chromatin plasticity and gene regulation. However, the processing, managing and mining of this huge volume of data require specialized computational tools and statistical methods that are yet to be standardized. Here, we describe a complete bisulfite sequencing analysis workflow, including recently developed programs, highlighting each of the crucial analysis steps required, i.e. sequencing quality control, reads alignment, methylation scoring, methylation heterogeneity assessment, genomic features annotation, data visualization and determination of differentially methylated cytosines. Moreover, we discuss the limitations of these technologies and considerations to perform suitable analyses.
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