How to extract cells of different species after mapping with combined genome?

Question

[vk]

I have samples from xenograft tumors with both human and mouse cells. Samples are from Singleron technology and I used celescope for preprocessing with human & mouse combined genome. From the QC I see there are 6k cells.

From the estimated number of cells, I would like to know how to get the number of mouse and human cells.

Any help is appreciated. Thank you.

[GenoMax]

You have used the tag snRNA-seq. I am not familiar with singleron tech but if you have sequence data you may be able to use xenome or bbsplit.sh to assign the reads to human/mouse bins. Unless there are cell specific barcodes it may not be possible to get the number of cells (which is what you are looking for).

https://singleron.bio/products/focuscope/ seems to indicate xenograft use case.

Answer 1

[Tony]

From the marker genes of each cluster, we can determine whether the cluster belongs to human or mouse. Human genes are all capitalized, while mouse genes only have the first letter capitalized. Just sum up the number of cluster cells belonging to human or mouse respectively.

[GenoMax]

Can you confirm that this answer is specific for singleron technology and associated bioinformatics software.

[Tony]

I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell species at the cluster level is simple, it cannot distinguish mutiplets. If you want to filter mutiplets, you can do it at the cell-level. For example:https://divingintogeneticsandgenomics.com/post/mixing-mouse-and-human-10x-single-cell-rnaseq-data/