BS-RNA An efficient mapping and annotation tool for RNA Bisulfite Sequencing data

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, rarely tools can directly deal with RNA bisulfite sequencing data efficiently at present. Hence, we have developed a specialized tool BS-RNA. Its annotation result is 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 supports both paired-end and single-end sequencing short reads from a directional bisulfite library. Evaluation results of the rates of uniquely mapped reads, rates of correctly mapped reads, and running time for simulated data and actual data indicate that BS-RNA can provide fast and accurate mapping of RNA bisulfite sequencing reads. Comparison between annotated cytosine methylation used BS-RNA and published research also shows that BS-RNA is an effective annotation tool for RNA bisulfite sequencing data.