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By default, all samples are used to perform QA/QC. If there is more than one sample, you You can choose to split the sample and perform QA/QC separately for each sample. 

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High-quality cells can be selected using the Selection card on the right Select & Filter, which is pre-loaded with three the selection rulescriteria, one for each quality metric (Figure 5).

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Hovering the mouse over one of the selection rules criteria reveals a histogram showing you the frequency distribution of the respective quality metric. The minimum and maximum thresholds can be adjusted by clicking and dragging the sliders sliders or by typing directly into the text boxes for each selection criteria (Figure 6).

Alternatively, Pin histogram to view all of the thresholds can be set by typing directly into the text boxes in each selection rule distributions at one time to determine thresholds with ease (Figure 7).

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Adjusting the selection criteria will select and deselect cells in all three plots simultaneously. Depending on your settings, the deselected points will either be dimmed or gray. The filters are additive. Combining multiple filters will include the intersection of the three filters. The number of cells selected is shown in the figure legend of each plot (Figure 8).

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To filter the high-quality cells, click the the include selected cells  icon in Filter in the Filtering card in the top right of Select & Filter, and click Apply observation filter... (Figure 9).

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Select the input data node for the filtering task and click Select (Figure 10).

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A new data node, Filtered counts, will be generated under the Analyses tab (Figure 11).

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Double click the Filtered counts data node to view the task report. The report includes a summary of the count distribution across all features for each sample; a detailed breakdown of the number of cells included in the filter for each sample; and the minimum and maximum values for each quality metric (expressed genes, total counts, etc) across the included cells for each sample (Figure 12).

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