How to filter out mouse cells to from a mixture library (mouse and human cells) by cellranger?
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!
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mzhoufulai •
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mzhoufulai •
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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.
Thank you! https://github.com/10XGenomics/cellranger/issues/24