Hello guys,

I am trying to analyze 10X scRNA-seq data and I am stuck at the QC stage. I have already mapped the reads to to the genome using Cell Ranger and removed EmptyDrops (empty cells) from the count matrix (using EmptyDrops). Now I want to use Scater [library(scater)] to perform an additional QC step below:

I want to keep only non empty cells that contain >= 40 genes and the cells should also contain >=500 total reads.

The instructions on the usage of this tool is only based on genome annotation and how to remove "potential dead cells - signified by high number of mitochondria). But have seen several papers where scater has been used to do something like the one I would want to do.

I do not know how to do this. Some one who can help please.

Thanks, Erick