title: BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data.
abstract: Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective experimental method for RNA cytosine methylation study. However, there are only a few tools can directly deal with RNA bisulfite sequencing data efficiently. Herein, we developed a specialized tool BS-RNA, which can analyze cytosine methylation of RNA based on bisulfite sequencing data and support both paired-end and single-end sequencing reads from directional bisulfite libraries. For paired-end reads, simply removing the biased positions from the 5' end may result in "dovetailing" reads, where one or both reads seem to extend past the start of the mate read. BS-RNA could map "dovetailing" reads successfully. The annotation result of BS-RNA is exported in BED (.bed) format, including locations, sequence context types (CG/CHG/CHH, H=A,T, or C), reference sequencing depths, cytosine sequencing depths, and methylation levels of covered cytosine sites on both Watson and Crick strands. BS-RNA is an efficient, specialized and highly automated mapping and annotation tool for RNA bisulfite sequencing data. It performs better than the existing program in terms of accuracy and efficiency. BS-RNA is developed by Perl language and the source code of this tool is freely available from the website: http://bs-rna.big.ac.cn.
authors.affiliation: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Liang
authors.affiliation: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Hao
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Jinyue
authors.initials: J
authors.lastname: Wang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Shuo
authors.initials: S
authors.lastname: Shi
authors.affiliation: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: xiaojf@big.ac.cn.
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.affiliation: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: lirj@big.ac.cn.
authors.forename: Rujiao
authors.initials: R
authors.lastname: Li
mesh_terms: D019175:DNA Methylation; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D013447:Sulfites / Q000737:chemistry*
chemical_list: D013447:Sulfites; D012313:RNA; C042345:hydrogen sulfite
keywords: Annotation tool; Bisulfite sequencing; Mapping software; RNA cytosine methylation