The Cell barcode QA/QC task lets you filter barcodes to differentiate between barcodes added to cells and barcodes added to empty gems or droplets in single cell RNA-Seq experiments. To invoke Cell barcode QA/QC: 

• Click a Single cell counts data node
• Click the QA/QC section of the task menu
• Click Cell barcode QA/QC 

The Cell barcode QA/QC task report is a plot (Figure 1). Barcodes are ordered on the X-axis by the number reads so that the barcode closest to the Y-axis has the most reads and the barcode furthest from the Y-axis has the fewest reads. The Y-axis value is the number of counts corresponding to each barcode. This type of plot is known as a knee plot. 

 

This plot is used to choose a cutoff point between barcodes that correspond to cells and barcodes that do not. Partek Flow automatically calculates a cutoff point, shown by the vertical line on the graph. Barcodes designated as cells are shown in blue while barcodes designated as without cells (background) are shown in grey. This cutoff can be adjusted by dragging the vertical line across the graph or by using the text fields in the Filter panel on the left-hand side of the plot. Using the Filter panel, you can specify the number of cells or the percentage of reads in cells and the cutoff point will be adjusted to match your criteria. The number of cells and the percentage of reads in cells is adjusted as the cutoff point is changed. To return to the automatically calculated cutoff, click Reset sample filter. 

The percentage of reads in cells and the median reads per cell are useful technical quality metrics that can be consulted when optimizing sample handling and cell isolation techniques. 

The Deduplication summary section indicates the number of initial and deduplicated alignments. 

 

 

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