How do I recalculate sequencing depth after filtering out beads that are not covered by tissue?
How do I recalculate sequencing depth after filtering out beads that are not covered by tissue?
- After you remove beads that are not covered by tissue, you can recalculate the sequencing depth using the following formula:
median number of reads per bead / median number of UMIs per bead
The "per bead" values of the "number of reads" and "number of UMIs" are located in the Seurat object metadata as $numReads and $nCount_RNA. Once you have determined the new "median reads/UMI" value, you can determine how saturated your sample was and calculate how much additional sequencing will be needed. We still recommend a value of 8–10 for this metric.