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Quality control of Cell Ranger filtered cells
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The Cell Ranger v1.3.1 software retains cells with similar UMI distributions72. We use this default threshold to obtain high-quality cells with large numbers of UMIs. After merging all samples, we filtered out cells that express <1000 genes. Furthermore, we exclude cells with more than 10% of reads mapping to the mitochondrial genome. These filtered data were used for all analyses except that presented in Fig. 4, Supplementary Figure 9a and Supplementary Data 7 where the EmptyDrops filtered cells (below) were utilised.
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