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Updated: Apr 1, 2026
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
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SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads
Neng Huang1,2, Heng Li3,4,
1Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
Nature Methods
|March 30, 2026
Summary
Long-read RNA sequencing tools are now available with longcallR, enabling accurate genetic variant analysis and the discovery of novel splicing events. This breakthrough facilitates deeper understanding of transcript structures and their links to genetic variations.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Long-read RNA sequencing offers potential for linking transcript structures to genetic variants.
- Current limitations include a lack of user-friendly analytical tools for this complex data.
Purpose of the Study:
- To introduce longcallR, a novel end-user tool for long-read RNA sequencing data analysis.
- To enable joint single-nucleotide polymorphism calling, haplotype phasing, and allele-specific analysis.
Main Methods:
- Development and application of the longcallR software package.
- Benchmarking of longcallR accuracy on established datasets.
- Analysis of 202 human samples using longcallR.
Main Results:
- longcallR demonstrates high accuracy in benchmark datasets.
- Identification of an average of 88 significant allele-specific splicing events per sample.
- Discovery that 46% of these events involved unannotated splice junctions.
Conclusions:
- longcallR provides a robust and accurate solution for analyzing long-read RNA sequencing data.
- The tool facilitates the discovery of novel allele-specific splicing events, including those with unannotated junctions.
- Enables deeper insights into the relationship between genetic variation and RNA splicing.
