Here is the things. I used the command 'cellbender remove-background --input /data/scratch/projects/punim1124/ZIWEI/Human_Spleen/spleen3/cellranger/outs/raw_feature_bc_matrix.h5 --output spleen3.1.output.h5 --expected-cells 500 --total-droplets-included 10000 --cuda --fpr 0.3
' to generate the CellBender matrix, and after comparing the output_filtered_seurat.h5 produced by cellbender to the raw_feature_bc_matrix.h5 produced by Cell Ranger, I noticed an increase in both the nCount and nFeature numbers of some part of cells. This seems unusual to me, and I’d like to get your thoughts on it. What do you think?
cellbender version is 0.3.2.
Looking forward to your reply.
Here is the things. I used the command 'cellbender remove-background --input /data/scratch/projects/punim1124/ZIWEI/Human_Spleen/spleen3/cellranger/outs/raw_feature_bc_matrix.h5 --output spleen3.1.output.h5 --expected-cells 500 --total-droplets-included 10000 --cuda --fpr 0.3 ' to generate the CellBender matrix, and after comparing the output_filtered_seurat.h5 produced by cellbender to the raw_feature_bc_matrix.h5 produced by Cell Ranger, I noticed an increase in both the nCount and nFeature numbers of some part of cells. This seems unusual to me, and I’d like to get your thoughts on it. What do you think?
cellbender version is 0.3.2. Looking forward to your reply.