L-GIREMI uncovers RNA editing sites in long-read RNA-seq
Zhiheng Liu, Giovanni Quinones-Valdez, Ting Fu, Elaine Huang, Mudra Choudhury, Fairlie Reese, A Mortazavi, Xinshu Xiao
Abstract
Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq.