This is a test version of Biostars. For the public version, visit https://www.biostars.org.
QC needed previous to DropletQC

I want to use for the first time DropletQC for analysis of single-cell RNA-sequencing data. I was reading through the vignette, and before applying identify_empty_drops() function to the example dataset, they mentioned "Each dataset has been pre-filtered using DropletUtils::emptyDrops and a 15% mitochondrial gene content cutoff". Is this the recommended workflow? I cannot find any more information regarding this step. I am confused about it as I thought you would either use DropletQC or emptyDrops. In addition, is it necessary to apply a mitochondrial content cut-off before DropletQC?

dropletqc
• 247 views • link
written by ae35f6e9 0

1 answer

emptyDrops removes empty droplets containing only ambient RNA, and the mitochondrial percentage filter depends on the cell type. Cells with high mitochondrial content may indicate poor sample quality or high metabolic activity, such as in cancer cells.

• 0 views • link
written by Arup Ghosh 402

If my initial workflow was CellRanger + SoupX + DropletQC ..., does it make sense to add emptyDrops? Is it a good workflow by itself?

• 0 views • link
written by ae35f6e9 0

If you are already removing ambient RNA and low-quality cells, you don't need to repeat the same with DropletUtils.

• 0 views • link
written by Arup Ghosh 402

Okay thanks!

• 0 views • link
written by ae35f6e9 0

Log in to answer this question.

More posts like this