is it normal to have zero mitochondria genes counts in my 10X data which is from Cellranger 5.0 count?
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7 weeks ago
FantasticAI ▴ 30

I'm trying to perform QC on my scRNAseq data which is from 10X, I find out there is zero mitochondria genes in my data, is this normal. I used the following code:

PercentageFeatureSet(data1101, pattern = "^mt-")

or

PercentageFeatureSet(data1101, pattern = "^MT-")

Both show zero.

10X scRNAseq • 308 views
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What organism is it, what reference genome are you using, what kit was used, and was it single nucleus RNA-seq?

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6 weeks ago
FantasticAI ▴ 30

Thank you for the comment, I just checked the data source, and they are single nucleus RNA seq, that is why they don't have any mitochondria genes

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It's great when the answer ends up being so simple. Thanks for following up!

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