ambient RNA quality control in scRNA-seq

Hi all,

In scRNA-seq analysis, nCount_RNA and nFeature_RNA value of one sample is very high compared to other samples. (below figure) Also, 'Fraction Reads in Cells' in this sample are 70.1%, but do not have a steep cliff in this sample's web summary (output of cell ranger).

1) So I wondering that this sample's quality was because of ambient RNA. If not, why? 2) Are there any other correction methods besides removing ambient RNA? 3) Would it be okay to do further analysis as it is without any corrections?

Thanks in advance!

Joonhong Kwon

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cellranger scrna-seq qc seurat snrna-seq

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written 3.1 years ago by joonhong kwon •

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