ScSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing.
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ABSTRACT: Identifying single nucleotide variants has become common practice for droplet-based single-cell RNA-seq experiments; however, presently, a pipeline does not exist to maximize variant calling accuracy. Furthermore, molecular duplicates generated in these experiments have not been utilized to optimally detect variant co-expression. Herein, we introduce scSNV designed from the ground up to "collapse" molecular duplicates and accurately identify variants and their co-expression. We demonstrate that scSNV is fast, with a reduced false-positive variant call rate, and enables the co-detection of genetic variants and A>G RNA edits across twenty-two samples.
SUBMITTER: Wilson GW
PROVIDER: S-EPMC8103760 | biostudies-literature |
REPOSITORIES: biostudies-literature
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