I am running CellBender 0.3.0 with default parameters. In one sample, the number of cells after processing through cellbender (N ~ 67000) are considerably more than output from cellranger (N ~ 9600 for filtered).
command:
cellbender remove-background --input raw_feature_bc_matrix.h5 --output ${FASTQ.ID}.cellbender.h5
The cellbender metrics, where most of the barcodes are considered to have cells looks like:
Hi,
I am running CellBender 0.3.0 with default parameters. In one sample, the number of cells after processing through cellbender (N ~ 67000) are considerably more than output from cellranger (N ~ 9600 for filtered). command:
cellbender remove-background --input raw_feature_bc_matrix.h5 --output ${FASTQ.ID}.cellbender.h5The cellbender metrics, where most of the barcodes are considered to have cells looks like:Thanks!