Do you check the relationship between nUMI vs nGenes plot? Do you have a specific threshold in this graph?

We do not explicitly check the relationship between nUMI and nGenes, but we do provide thresholds to remove genes with too high or too low nUMI or nGenes. In order to deal with the variety of datasets Basepair receives, we use the simple approach of removing cells that are +/- 3 standard deviations away from the median for nUMI and nGenes, separately. However, you can override these default thresholds with your own.