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[Preprint]. 2023 Sep 15:2023.09.14.543267.
doi: 10.1101/2023.09.14.543267.

Universal preprocessing of single-cell genomics data

A Sina Booeshaghi  1 , Delaney K Sullivan  1   2 , Lior Pachter  1   3
Affiliations

Universal preprocessing of single-cell genomics data

A Sina Booeshaghi et al. bioRxiv. .

Abstract

We describe a workflow for preprocessing a wide variety of single-cell genomics data types. The approach is based on parsing of machine-readable seqspec assay specifications to customize inputs for kb-python, which uses kallisto and bustools to catalog reads, error correct barcodes, and count reads. The universal preprocessing method is implemented in the Python package cellatlas that is available for download at: https://github.com/cellatlas/cellatlas/.

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Figures

Figure 1:
Figure 1:
Single-cell genomics assays are variations on a theme of physical isolation, molecular capture, and library generation. The read structure shown here is provided as an example; read structure may vary depending on assay type.
Figure 2:
Figure 2:
Efficiency of UMI detection as measured by relating the number of reads uniquely aligned for each cell to the number of UMIs for the a) RNA, b) protein, and c) tag modalities.
Figure 3:
Figure 3:
Cross-technology comparison of registered ATAC and RNA quantifications from PBMCs assayed with (a) DOGMA-seq and (b) 10x Multiome.
See this image and copyright information in PMC

References

    1. Battenberg Kai, Thomas Kelly S., Ras Radu Abu, Hetherington Nicola A., Hayashi Makoto, and Minoda Aki. 2022. “A Flexible Cross-Platform Single-Cell Data Processing Pipeline.” Nature Communications 13 (1): 6847. - PMC - PubMed
    1. Booeshaghi A. Sina, Chen Xi, and Pachter Lior. 2023. “A Machine-Readable Specification for Genomics Assays.” bioRxiv : The Preprint Server for Biology, March. 10.1101/2023.03.17.533215. - DOI - PMC - PubMed
    1. Booeshaghi A. Sina, Yao Zizhen, van Velthoven Cindy, Smith Kimberly, Tasic Bosiljka, Zeng Hongkui, and Pachter Lior. 2021. “Isoform Cell-Type Specificity in the Mouse Primary Motor Cortex.” Nature 598 (7879): 195–99. - PMC - PubMed
    1. Bray Nicolas L., Pimentel Harold, Melsted Páll, and Pachter Lior. 2016. “Near-Optimal Probabilistic RNA-Seq Quantification.” Nature Biotechnology 34 (5): 525–27. - PubMed
    1. Cao Junyue, Packer Jonathan S., Ramani Vijay, Cusanovich Darren A., Huynh Chau, Daza Riza, Qiu Xiaojie, et al. 2017. “Comprehensive Single-Cell Transcriptional Profiling of a Multicellular Organism.” Science 357 (6352): 661–67. - PMC - PubMed

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