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ScSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing.

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 | 2021 May

REPOSITORIES: biostudies-literature

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scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing.

Wilson Gavin W GW Derouet Mathieu M Darling Gail E GE Yeung Jonathan C JC

Genome biology 20210507 1

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 ...[more]

PMID: 33962667

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