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Update README.md
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AlicenJoyHenning authored Sep 22, 2024
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Expand Up @@ -18,7 +18,7 @@ Single-cell RNA sequencing (scRNA-seq) is a well-established technique in the er

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For droplet-based protocols, ‘low quality’ cells are those that originate from droplets that contain either more than one cell (doublet), no cells (empty), or a damaged cell. While many quality control tools available are designed to identify doublets and empty droplets, few are specialised in identifing damaged cells. Damaged cell detection is more often achieved by setting thresholds for metrics such as average mitochondrial gene expression or UMI and features counts per barcode. These thresholds, even when dynamically calculated, vary across samples, cell types, tissues, treatment conditions, and species. This could result in overly stringent filtering, where many true cells are excluded from downstream but also in overly conservative filtering where many contaminating damaged cells remain. But searching for true damaged droplets in a sample-specific manner is tedious and not always intuitive, leading to user-defined filtering that lacks reproducibility.
For droplet-based protocols, ‘low quality’ cells are those that originate from droplets that contain more than one cell (doublet), no cells (empty), or a damaged cell. While quality control tools are available to identify doublets and empty droplets, few are specialised in identifing damaged cells. Damaged cell detection is more often achieved by setting thresholds for metrics such as average mitochondrial gene expression or UMI and features counts per barcode. These thresholds, even when dynamically calculated, vary across samples, cell types, tissues, treatment conditions, and species. This could result in overly stringent filtering, where many true cells are excluded from downstream analysis, or, in overly conservative filtering, where many contaminating damaged cells remain. But searching for true damaged droplets in a sample-specific manner is tedious and not always intuitive, leading to user-defined filtering that lacks reproducibility.

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