How to filter out mouse cells to from a mixture library (mouse and human cells) by cellranger?

Question

[mzhoufulai]

Hi, I am new in single-cell RNA-seq. I got a library with a mixture of human and mouse cells. The mouse cells ratio is only 2.5%. I used cellranger count to get the matrix. But the output of cellranger count is a mix of human and mouse. How I can filter out mouse cells and only get a matrix of human cells? Thanks!

[GenoMax]

You may have to do three runs (human, mouse and human+mouse) to see what the counts look like. I suggest that you ask 10x tech support if they have a recommended way of dealing with this.

[am]

Thank you! https://github.com/10XGenomics/cellranger/issues/24

Answer 1

[swbarnes2]

What reference did you align to? Last time I used the combined human/mouse reference that 10x provided, I thought I got a separate set of files for each species.