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...
Gespeichert in:
| Hauptverfasser: | , , , , , , |
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| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
31 August 2023
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| In: |
BMC bioinformatics
Year: 2023, Jahrgang: 24, Heft: 1 |
| ISSN: | 1471-2105 |
| DOI: | 10.1186/s12859-023-05440-8 |
| Online-Zugang: | Verlag, kostenfrei, Volltext: https://doi.org/10.1186/s12859-023-05440-8
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| Verfasserangaben: | John K.L. Wong, Lena Jassowicz, Christel Herold-Mende, Martina Seiffert, Jan-Philipp Mallm, Peter Lichter, Marc Zapatka |
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| 520 | |a 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. | ||
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| 650 | 4 | |a Sample pooling | |
| 650 | 4 | |a Single nucleotide polymorphisms | |
| 650 | 4 | |a Single-cell | |
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