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

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 sampl...

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Bibliographic Details
Main Authors: Wong, John K. L. (Author) , Jassowicz, Lena (Author) , Herold-Mende, Christel (Author) , Seiffert, Martina (Author) , Mallm, Jan-Philipp (Author) , Lichter, Peter (Author) , Zapatka, Marc (Author)
Format: Article (Journal)
Language:English
Published: 31 August 2023
In: BMC bioinformatics
Year: 2023, Volume: 24, Issue: 1
ISSN:1471-2105
DOI:10.1186/s12859-023-05440-8
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1186/s12859-023-05440-8
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Author Notes:John K.L. Wong, Lena Jassowicz, Christel Herold-Mende, Martina Seiffert, Jan-Philipp Mallm, Peter Lichter, Marc Zapatka
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Summary: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.
Item Description:Gesehen am 31.10.2023
Physical Description:Online Resource
ISSN:1471-2105
DOI:10.1186/s12859-023-05440-8

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