I'm analyzing 10x scRNA-seq data generated from xenografts (mouse + human tissues). I have the following workflow to label cells as either mouse or human:
- Align 10x scRNA-seq data to mouse+human combined genome using cellranger count.
- Use the file generated by cellranger count (gem_classification.csv) which assigns mouse, human, or multiplet to each cell to classify each cell type.
- Realign the fastq files to the mouse genome ( we are interested in the mouse cells) using cellranger count
- Use the classification from Step 2 to filter out human cells in Seurat.
Would this be the right approach or is there a better alternative that you would recommend?
Thanks a lot!