CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

Publication date: Available online 3 January 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xu-Kai Ma, Meng-Ran Wang, Chu-Xiao Liu, Rui Dong, Gordon G. Carmichael, Ling-Ling Chen, Li YangAbstractSequences of circular RNAs (circRNAs) produced from back-splicing of exon(s) completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction (BSJ) sites. Therefore, examination of global circRNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites, which is different from the quantification of linear RNA expression by normalized RNA-seq fragments mapped to whole gene bodies. Thus, direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained challenging. Here, we update the previously-reported CIRCexplorer pipeline to version 3 for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq (CIRCexplorer3-CLEAR). A new quantitation parameter, fragments per billion mapped bases (FPB), is applied to evaluate circular and linear RNA expression individually by fragments mapped to circRNA-specific BSJ sites or to linear RNA-specific splicing junction (SJ) sites. Comparison of circular and linear RNA expression levels is directly achieved by dividing FPBcirc by FPBlinear to generate a CIRCscore, which indicates the relative circRNA expression level using linear RNA expressio...

Source: Genomics, Proteomics and Bioinformatics - January 15, 2020 Category: Bioinformatics Source Type: research