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An efficient, specialized and highly automated mapping and annotation tool for RNA bisulfite sequencing data. Focusing on both CG and non-CG methylation, BS-RNA can handle the mapping and annotation of either single- or paired-end sequencing reads of directional bisulfite libraries. This tool provide more comprehensive annotation information such as the distribution of cytosine methylation in both gene and transcript levels.

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BS-RNA versioning

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BS-RNA classification

BS-RNA specifications

Software type:
Restrictions to use:
Output data:
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.
Operating system:
Computer skills:
Command line interface
Input data:
RNA bisulfite sequencing data
Output format:
Programming languages:
Python, HISAT2, SAMtools, Bowtie2

BS-RNA support



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BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China

Funding source(s)

This study was supported by grant from the National Programs for High Technology Research and Development (863 Program; 2012AA020409, 2015AA020108), the Ministry of Science and technology of the People’s Republic of China; grant from the National Science Foundation of China (No. 31271386, No. 31100915 and No. 31471248).

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