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Article

scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis.

BMC bioinformatics - 31 Aug 2023

Wong John K L, Jassowicz Lena, Herold-Mende Christel, Seiffert Martina, Mallm Jan-Philipp, Lichter Peter, Zapatka Marc

Abstract excerpt

BACKGROUND: Here we present scSNPdemux, a sample demultiplexing pipeline for single-cell RNA sequencing data using natural genetic variations in humans. The pipeline requires alignment files from Cell Ranger (10× Genomics), a population SNP database and genotyped single nucleotide polymorphisms (SNPs) per sample. The tool works on sparse genotyping data in VCF format for sample identification. RESULTS: The...

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PMID: 37653401
DOI: 10.1186/s12859-023-05440-8
PMCID: PMC10469441

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