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I have 10X scRNA-seq multiome's 3' poly-A capture (scRNA-seq+ATAC-seq) from PBMC

Using Seuratreference mapping, I mapped my scRNA-seq part on reference PBMC (for cell type annotation)

I have also tried Seurat zimuth shiny app

But likely just a few of my cells has been mapped on the reference

Please look at this

enter image description here

Do you think this because my data is multiome or something else is going wrong?

Please any body has some experience help me

Thank you

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Yes! Multiome seems to have cells with much higher mitochondrial gene content. I don't understand the biology behind this. But in using a cut off of 5% (i.e. remove cells with >5% MT genes) I lose over 80% of cells in multiome data. Also, here is the Signac tutorial where they use a 20% cut off for multiome data - https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html ("WNN analysis of 10x Multiome, RNA + ATAC")

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As I mentioned in my answers to similar questions, there are a lot of cells with very high mitochondrial gene content. It would be a good idea to work out why that is before doing any more downstream processing.

These cells will, of course, be filtered out by the thresholds you have set.

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