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.
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 usexenome
orbbsplit.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.