My goal is to get an expression matrix with gene expression values for each cell without any mouse cells in there. I need to analyze single-cell data from a PDX tumor.
I have read papers about the tools for deconvolution of mouse and human genes from PDX tumors. However, I am not sure if they can be applied to single-cell data.
I have fastq files with sc RNA-seq, I aligned them separately to mouse and human references using STAR. I used the resulting . bam files as an input in XenofilteR to filter out mouse reads. Then I tried to quantify the resulting filtered .bam file using featureCounts from this tutorial. But the output expression matrix did not have cell columns.
I will appreciate if you share any concerns or advice.