loom contains significantly less cells than those in "filtered_feature_bc_matrix"

[Lei-Guo]

Hi,

I found the loom files generated by loompy contain much less cells (80% less) than those called by cellranger (e.g., "filtered_feature_bc_matrix"). This is quite significant. I also noticed a warning in the standard out file during the "Calling cells" process: "WARNING - No ambient RNA beads were found; maybe sample had too few cells?".

How do I solve this problem?