single cell RNA sequencing and mitochondrial percent
1
1
Entering edit mode
4 months ago
kayah ▴ 20

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!

mitochondria scRNAseq • 408 views
ADD COMMENT
1
Entering edit mode
4 months ago
tothepoint ▴ 930

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

ADD COMMENT
1
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1446 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6