CIRCexplorer3:A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression
- Author:
Ma XU-KAI
1
;
Wang MENG-RAN
;
Liu CHU-XIAO
;
Dong RUI
;
Carmichael G. GORDON
;
Chen LING-LING
;
Yang LI
Author Information
1. CAS Key Laboratory of Computational Biology
- Keywords:
Circular RNA;
Back-splicing;
Linear RNA;
Pre-mRNA splicing;
Ribo-RNA-seq
- From:
Genomics, Proteomics & Bioinformatics
2019;17(5):511-521
- CountryChina
- Language:Chinese
-
Abstract:
Sequences of circular RNAs (circRNAs) produced from back-splicing of exon(s) com-pletely 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 span-ning 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 newquantitation 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 expression level as the background. Highly-expressed circRNAs with low cognate linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further investigation. CIRCexplorer3-CLEAR is publically avail-able at https://github.com/YangLab/CLEAR.
