This file contains three plots, which visualize barcode distribution and include details on cell uniformity and amplicon distribution. It is index-specific, meaning for only one tube.
To calculate the threshold, we first create a subset of barcodes from all the barcodes in the barcode.cell.distribution.tsv file by keeping the barcodes that have total reads greater than the number of amplicons * 10. Next, we calculate the mean reads per barcode per amplicon from the kept barcodes. The threshold is then set to either 10 or 0.2 * the mean, whichever is smaller.
Total Reads vs Rank-Ordered Barcodes
This is a log-log plot. The y-axis is Log10 Total Reads with the number of reads for each barcode. The x-axis has the barcodes ranked in order with those having the most reads on the left.
The vertical line represents the threshold where we call cells.
Cell Uniformity per Amplicon
This waterfall plot looks at cell uniformity. The y-axis is the percentage of amplicons above the threshold. The x-axis is the number of cells per amplicon.
The horizontal bar is at the 80 % threshold. The vertical line is where the horizontal line intersects the plot.
Below the plot is the calculation of the percentage of the cells within the vertical and horizontal lines, meaning cells complete. The y-axis label displays the calculated threshold.
Amplicon Uniformity per Cell
This plot looks at amplicon uniformity. The y-axis is the percentage of cells above the threshold. The x-axis contains the amplicons sorted by mean reads.
The amplicons in blue passed the threshold. The ones in red failed. The chart title lists the number of failed amplicons as well as the calculated threshold.