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L-GIREMI uncovers RNA editing sites in long-read RNA-seq.

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.

SUBMITTER: Liu Z

PROVIDER: S-EPMC10360234 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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L-GIREMI uncovers RNA editing sites in long-read RNA-seq.

Liu Zhiheng Z Quinones-Valdez Giovanni G Fu Ting T Huang Elaine E Choudhury Mudra M Reese Fairlie F Mortazavi Ali A Xiao Xinshu X

Genome biology 20230720 1

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 identificat ...[more]

PMID: 37474948

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