WBSA: Web Service for Bisulfite Sequencing Data Analysis

PLOS ONE, Dec 2019

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.

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WBSA: Web Service for Bisulfite Sequencing Data Analysis

Citation: Liang F, Tang B, Wang Y, Wang J, Yu C, et al. ( WBSA: Web Service for Bisulfite Sequencing Data Analysis Fang Liang. 0 Bixia Tang. 0 Yanqing Wang 0 Jianfeng Wang 0 Caixia Yu 0 Xu Chen 0 Junwei Zhu 0 Jiangwei Yan 0 Wenming Zhao 0 Rujiao Li 0 Matteo Pellegrini, UCLA-DOE Institute for Genomics and Proteomics, United States of America 0 Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , China 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. - Funding: This work was supported by the Natural Science Foundation of China (31000584 to RL), (http://www.nsfc.gov.cn/Portal0/default152.htm); and the Apparatus Function Innovation Program of the Chinese Academy of Sciences (201212 to WZ), (http://www.cas.cn/); The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. DNA methylation plays an important role in cell differentiation, X chromosome inactivation, genomic imprinting through regulation of transcription, chromatin structure, chromosome stability, and tumorigenesis [1,2,3,4,5,6]. DNA methylation research has been accelerated by the development of next-generation sequencing technology, and it is now the focus of research groups with diverse interests [5,7,8,9,10,11,12]. There are four mainstream sequencing-based methods for DNA methylation profiling: two utilize enrichment of methylated DNA (Methylated DNA Binding Domain sequencing, or MBD-seq [7] and Methylated DNA Immunoprecipitation sequencing, or MeDIP-seq [8,9]), and the other two utilize bisulfite conversion (MethylC-seq or WGBS [10] and Reduced Representation Bisulfite Sequencing or RRBS [11]). Reacting DNA with bisulfite converts cytosine residues to uracil residues but does not alter 5-methylcytosine residues, which makes it possible to distinguish methylated from unmethylated cytosine residues. Because bisulfite sequencing determines single base changes, its resolution is greater than those methods that utilize DNA enriched in methylated regions [12]. WGBS and RRBS are widely used in biological research [5,12]. The read alignment of bisulfite sequencing data differs from that generated using non-bisulfite sequencing due to the change of C to T residues. Therefore, alignment tools such as BSMAP [13], BS SEEKER [14], RMAP [15], and Bismark [16] were developed to address this issue. Further, common alignment tools such as BWA [17] and Bowtie [18,19] also align bisulfite sequencing reads to a reference sequence after the reads and the reference sequences have been converted [10]. Other tools are available for analyzing bisulfite sequencing data, such as CyMATE [20], CpG PatternFinder [21], GBSA [22], COHCAP [23], methylKit [24], and BSmooth [25]. Their applications are limited because their analytical pipelines either require aligned reads as input or only support single-end alignments. Moreover, these tools only identify methylated cytosines or only analyze methylated CpG islands to search for correlations between methylation and gene expression. SAAP-RRBS [26] and RRBS-Analyser [27] integrated BSMAP as an alignment tool and acted as streamlined analysis and annotation pipelines. However, these approaches are designed only for RRBS data with limited annotations. Certain tools identify differentially methylated regions [24,25,27,28], but most do not focus on analysis of non-CGs (Table 13). We describe here WBSA, which provides a user-friendly and novel web service for analyzing bisulfite sequencing data. WBSA focuses on the analysis of CpG as (...truncated)


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Fang Liang, Bixia Tang, Yanqing Wang, Jianfeng Wang, Caixia Yu, Xu Chen, Junwei Zhu, Jiangwei Yan, Wenming Zhao, Rujiao Li. WBSA: Web Service for Bisulfite Sequencing Data Analysis, PLOS ONE, 2014, 1, DOI: 10.1371/journal.pone.0086707