WBSA: web service for bisulfite sequencing data analysis

• Published in: PloS one Vol. 9; no. 1; p. e86707
• Main Authors: Liang, Fang, Tang, Bixia, Wang, Yanqing, Wang, Jianfeng, Yu, Caixia, Chen, Xu, Zhu, Junwei, Yan, Jiangwei, Zhao, Wenming, Li, Rujiao
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30.01.2014; Public Library of Science (PLoS)
• Subjects: Animals; Annotations; Bioinformatics; Biology; Bisulfite; Chromosome Mapping; CpG islands; Data analysis; Data processing; Deoxyribonucleic acid; DNA; DNA Methylation; DNA sequencing; Gene expression; Gene mapping; Gene sequencing; Genes; Genome, Human; Genomes; Genomics; High-Throughput Nucleotide Sequencing; Humans; Identification; Information management; Internet; Mathematics; Methylation; Modules; Molecular Sequence Annotation; Oocytes; Pipelines; Plants (botany); Quality; Sequence Analysis, DNA; Software; Stem cells; Sulfites; Sulfites - chemistry; Web services; Web sites (World Wide Web); Beijing China; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0086707

Whole-Genome Bisulfite Sequencing (WGBS) and genome-wide Reduced Representation Bisulfite Sequencing (RRBS) are widely used to study DNA methylation. However, data analysis is complicated, lengthy, and hampered by a lack of seamless analytical pipelines. To address these issues, we developed a convenient, stable, and efficient web service called Web Service for Bisulfite Sequencing Data Analysis (WBSA) to analyze bisulfate sequencing data. WBSA focuses on not only CpG methylation, which is the most common biochemical modification in eukaryotic DNA, but also non-CG methylation, which have been observed in plants, iPS cells, oocytes, neurons and stem cells of human. WBSA comprises three main modules as follows: WGBS data analysis, RRBS data analysis, and differentially methylated region (DMR) identification. The WGBS and RRBS modules execute read mapping, methylation site identification, annotation, and advanced analysis, whereas the DMR module identifies actual DMRs and annotates their correlations to genes. WBSA can be accessed and used without charge either online or local version. WBSA also includes the executables of the Portable Batch System (PBS) and standalone versions that can be downloaded from the website together with the installation instructions. WBSA is available at no charge for academic users at http://wbsa.big.ac.cn.