Use of Scater for QC in scRNA-seq Analysis: How to remove cells with less than certain number of genes supported with certain number of reads

Question

[otieno43]

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 have tried to figure out what could be done, I have realized am not making any head ways, so I will not post a crappy script (in short I do not know how to do this). Some one who can help please, even with a putative script that can customize.

Thanks, Erick

Answer 1

[ATpoint]

If you use scater or scuttle it's really just simple subsetting:

library(scuttle)

sce <- scuttle::addPerCellQCMetrics(sce)

minimum_genes <- 40
minumum_total <- 500

sce[,sce$detected > minimum_genes & sce$total > minimum_total]

[otieno43]

Thanks let me try and see how it goes.