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Quality singles

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Online ahead of print. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control QC metrics. Current best practices use these QC metrics independently with either arbitrary, uniform thresholds e. Current practices are often overly stringent and especially untenable on certain types of tissues, such as archived tumor tissues, or tissues associated with mitochondrial function, such as kidney tissue [1]. We propose a data-driven QC metric miQC that jointly models both the proportion of reads mapping to mtDNA genes and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses.

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