Partek Flow Documentation

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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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SubtitleTextSelect & Filter criteria
AnchorNameSelect & Filter Single cell QAQC

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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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SubtitleTextUse the sliders and histograms to adjust the selection criteria
AnchorNameSelecting cells using sliders

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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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SubtitleTextPin the histogram to view all of the distributions at one time
AnchorNamePin histogram

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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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SubtitleTextThe figure legends show 3696/4352 cells with total count <12,000, number of detected features 600 - 2500, and % mitochondrial count <5% are selected in all three plots. Selected cells are blue, filters are additive and deselected cells are dimmed.
AnchorNameSingle cell QAQC with selection criteria applied

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To filter the high-quality cells, click the 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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SubtitleTextAfter the Apply filter button is selected, you will be presented with a preview of your pipeline. You need to select the appropriate data node to apply the filtering to
AnchorNameSelect input data node for filtering

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

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SubtitleTextFilter cells task runs from the Single cell QA/QC report
AnchorNameOutput of Single cell QA/QC

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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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SubtitleTextFiltered counts task report
AnchorNameFilter counts report

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Additional assistance


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