Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite

MOTIVATION: RNA 5-methylcytosine (m(5)C) is a type of post-transcriptional modification that may be involved in numerous biological processes and tumorigenesis. RNA m(5)C can be profiled at single-nucleotide resolution by high-throughput sequencing of RNA treated with bisulfite (RNA-BisSeq). However, the exploration of transcriptome-wide profile and potential function of m(5)C in splicing remains to be elucidated due to lack of isoform level m(5)C quantification tool. RESULTS: We developed a computational package to quantify Epitranscriptomal RNA m(5)C at the transcript isoform level (named Episo). Episo consists of three tools: mapper, quant and Bisulfitefq, for mapping, quantifying and simulating RNA-BisSeq data, respectively. The high accuracy of Episo was validated using an improved m(5)C-specific methylated RNA immunoprecipitation (meRIP) protocol, as well as a set of in silico experiments. By applying Episo to public human and mouse RNA-BisSeq data, we found that the RNA m(5)C is not evenly distributed among the transcript isoforms, implying the m(5)C may subject to be regulated at isoform level. AVAILABILITY AND IMPLEMENTATION: Episo is released under the GNU GPLv3+ license. The resource code Episo is freely accessible from https://github.com/liujunfengtop/Episo (with Tophat/cufflink) and https://github.com/liujunfengtop/Episo/tree/master/Episo_Kallisto (with Kallisto). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.