Use of Scater for QC in scRNA-seq: How to remove cells with less than certain number of genes supported with certain number of reads
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otieno43 • 0
@aa5bab85
Last seen 6 days ago
United States

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

SingleCellExperiment • 95 views
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