Single-Cell RNA

Single Cell RNA Metrics

Metric	Description
Total Reads	Total number of reads for the sample
% Mapped	Percentage of reads that are mapped to the genome
Reads with Valid Barcodes	Number of reads with barcodes that match the whitelist
Passing Cells	Number of barcodes associated with at least one cell
% Reads in Passing Cells	Percentage of reads that contain a valid barcode
Median Reads per Cell	The median number of reads detected per cell-associated barcode
Median Molecules per Cell	The median number of molecules detected per cell-associated barcode
Median Genes per Cell	The median number of genes detected per cell-associated barcode
% Sequencing Saturation	The percentage of the total cDNA library that has been observed at a given sequencing depth

Barcode Rank Plot

The barcode rank plot (often referred to as the “knee plot”), orders barcodes based on the number of transcripts associated with them. Typically, the cell barcodes are concentrated at the top of the rank plot, whereas the background barcodes are concentrated in the lower portion of the plot. The purpose of the cell calling is to find a point in the first “knee” area that separates the cells from the background.

Barcode Summary Metrics

Metric	Description
Cell Type	“PASS” for passing cells or “LOW” for background cells
Total Reads	Total number of reads for the cell type
Total Barcodes	Total number of barcodes for the cell type
Transcripts	Total number of transcripts for the cell type
Gene Reads	Total number of reads that map to a gene in the transcriptome for the cell type
Mitochondrial Reads	Total number of reads that map to mitochondrial transcripts for the cell type. This is based on gene names that include prefixes like “MT-” and may not work with every mapping reference
Genes	Total number of genes for the cell type

UMAP Plot

The UMAP plot allows visualization of individual cells in 2D space to capture the similarities between cells. Clustering is performed using the Louvain method.