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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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Hovering the mouse over one of the selection 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 or by typing directly into the text boxes for each selection criteria (Figure 6).

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Alternatively, Pin histogram to view all of the 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 include selected cells  icon in Filter in the top right of Select & Filter, and click Apply observation filter... (Figure 9).

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

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