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- Expand the QA/QC section of the task menu
- Click on Single cell QA/QC (Figure 6) Do and do not choose to split by sample
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The Single cell QA/QC report opens in a new data viewer session. There are interactive violin plots showing the most commonly used quality metrics for each cell from all samples combined (Figure 8). For this data set, there are two relevant plots: the total count per cell and the number of detected genes per cell. Each point on the plots is a cell and the violins illustrate the distribution of values for the y-axis metric. Typically, there is a third plot showing the percentage of mitochondrial counts per cell, but mitochondrial transcripts were not included in the data set by the study authors, so this plot is not informative for this data set.
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The plots are highly customizable and can be used to explore the quality of cells in different samples.
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