Question: When I hover my cursor over the barcode rank plot, a box appears with percentages - what do these refer to?
Answer: The values that pop-up in the barcode rank plot show the proportion of barcodes that were called as cells during the cell calling algorithm for a given UMI range. Below is an example of how to interpret two different percentage values that pop-up while hovering over data points on a barcode rank plot.
The blue color gradient is proportional to the fraction of cells in a given subset of barcodes, where darker blue indicates a higher proportion of barcodes called as cells. During step one of the cell calling algorithm for single cell gene expression, Cell Ranger estimates the barcodes likely to contain an intact cell (dark blue). In step two of the cell calling algorithm, it distinguishes background barcodes from those containing a cell, resulting in a fraction of barcodes called as cells and the rest as background (lighter blue). You can read more about this process on our algorithms page.
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Targeted Gene Expression