Single-Cell RNA

Single Cell RNA Metrics

Metric	Description
Total Input Reads	Total number of reads for the sample
% Mapped	Percentage of reads that are mapped to the genome
Total Barcoded Reads	Number of reads with barcodes that match the whitelist
Passing Cells	Total unique barcodes that pass the count threshold for a passing cell
% Reads in Passing Cells	Number of reads in passing barcodes divided by the total number of reads in all cells of barcodes
Mean Reads per Cell*	Mean reads per cell (Total gene reads / Passing cells)
Median Reads per Cell	The median number of reads per passing barcode
Median Molecules per Cell	The median number of captured RNAs per passing barcode
Median Genes per Cell	The median number of unique genes identified per passing barcode
% Sequencing Saturation	Percentage chance that if you sequenced an additional read, it would have already been observed at least once

*Only available for analyses with PIPseq CRISPR mode enabled

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.

Extended Single-Cell RNA Metrics

This section is only available for analyses with PIPseq CRISPR mode enabled.

Metric	Description
Input Gene Expression Reads	Total input gene expression reads
Input Feature Reads	Total input feature reads
Barcoded Gene Expression Reads	Total barcoded gene expression reads
Barcoded Feature Reads	Total barcoded feature reads
Unique Exon Reads	Unique exon matching reads
Unique Intron Reads	Unique intron matching reads
Filtered Antisense Reads	Filtered antisense reads
Filtered Ambiguous Reads	Filtered ambiguous reads
Filtered Low MAPQ Reads	Filtered low MAPQ reads
Filtered Non-Matching Reads	Filtered non-matching reads
Mitochondrial Reads	Mitochondrial reads
Total Gene Reads	Total gene reads
Counted Gene Reads	Total counted genes
Molecules	Total molecules
Genes Detected	Total genes detected

Barcode Summary Metrics

Metric	Description
Cell Type	Barcode classification category. “PASS” for passing cells or “LOW” for background cells.
Total Gene Reads	Total number of genic reads in the category
Molecules	Total number of molecules in the category
Genes	Total number of unique genes detected for each cell in the category
Mitochondrial Reads	Total number of mitochondrial reads in the category. This is based on gene names that include prefixes like “MT-” and may not work with every mapping reference.
Feature Molecules*	Total number of CRISPR or other target molecules in the category
Features*	Total number of unique CRISPR sequences or other targets detected in the category

*Only available for analyses with PIPseq CRISPR mode enabled

Feature Metrics

This section is only available for analyses with PIPseq CRISPR mode enabled.

Metric	Description
Input Feature Reads	Total input feature reads
Barcoded Feature Reads	Total barcoded feature reads
Feature Matching Reads	Feature matching reads
Feature Reads	Total Feature Reads
Feature Molecules	Total feature molecules
Median Feature Reads per Cell	Median feature reads per passing cell
Feature Molecules per Cell	Median feature molecules per passing cell
Features per Cell	Median features per passing cell
Features Detected	Total features detected
CRISPR Reads	Total CRISPR reads matching known barcodes
% Mapped Features	Percentage of CRISPR tags mapped
% Features in Cells	Percentage of valid CRISPR tags in cells
% Cells with Features	Percentage passing cells with CRISPR reads