Question: What proportion of cells do you get both good ATAC and good Gene Expression data?
Answer: As part of the web summary file, the cross-sensitivity plot shows RNA UMIs per barcode in the y-axis and transposition events in peaks per barcode in the x-axis (i.e. RNA and ATAC data for each cell).
Cells are expected to be located at the upper right-hand corner with high RNA and high ATAC data. A clear separation between cells and non-cells (empty GEMs, background signal) should also be observed. In the example above, from the 3k PBMCs public dataset, you observe strong ATAC and RNA data for most cells, with only a few cells showing lower ATAC or lower GEX.
Products: Single Cell Multiome ATAC + Gene Expression