Hi, I am new to scRNA seq and I'd need help with this. I have a rat sample containing a human xenograft (around 5% of total cells are human). I am only interested in the human cells. Talking to 10x reps, they recommended this approach
1) I created a rat+human genome, mapped the 10x output to the human+ rat genome and to the human genome only.
2) I should subtract from the human only mapped output, the cells that previously mapped to rat, based on their barcode.
I am not quite sure how to do this, how to eliminate cells based on the barcode. Any help would be highly appreciated!
You're going to need to dig deep into the output files from CellRanger count to understand how to exclude cells by barcode. I also work on 10X platforms + xenografts but I follow a different approach. It kinda intuitively makes sense to me but I'd also love others' takes on it.
Use software like Xenome or BBSplit to split the biological reads (R2 for scRNAseq, R1 & R3 for scATACseq etc.) to split these into reads that fall into human, mouse and other ambiguous categories (if applicable).
Using BBMap's filterbyname.sh, extract non-transcriptome reads (I1, I2, R1, R2 etc. as applicable) to match the above split transcriptome reads so you have matching I and R read files for each organism.
Use the sets generated above to map to the 10X organism-specific index.
