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scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
- Publication Year :
- 2022
- Publisher :
- Cold Spring Harbor Laboratory, 2022.
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Abstract
- Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single-nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq dataset, scAllele identified variants with strong allelic linkage to alternative splicing, some of which are cancer specific and enriched in cancer-relevant pathways. scAllele represents a versatile tool to uncover multilayer information and previously unidentified biological insights from scRNA-seq data.
- Subjects :
- Multidisciplinary
Subjects
Details
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....3daf8911479d5d0339bdfe315b86f691