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Comput Biol Chem. 2016 Dec;65:173-177. doi: 10.1016/j.compbiolchem.2016.09.003. Epub 2016 Sep 9.

BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data.

Author information

1
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
2
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.
3
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.
4
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: lirj@big.ac.cn.

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.

KEYWORDS:

Annotation tool; Bisulfite sequencing; Mapping software; RNA cytosine methylation

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