single cell RNA sequencing and mitochondrial percent

Question

[kayah]

Hello I want to know criterion of mitochondrial percent in scRNAseq I know that too high percentage means no good cell quality but i don't understand it's criterion.. If i analyze some tissue it contains variety of cells so I don't get which criterion suits for scRNAseq. If you know about this please tell me about it thank you!

Answer 1

[tothepoint]

You can read this post mt percent where jared.andrews07 already shared the response.

[jared.andrews07]

See this post for some additional comments (on other QC metrics, but the same logic applies - blanket thresholding approaches have some drawbacks).

[Zhenyu Zhang]

There are caveats. For example, cardiomyocytes can have very high MT gene expression.

This is definitely a very important and efficient filter I will definitely include in hands-on analysis; However, I am hesitating to integrate this into an automatic pipeline without checking the plot.