Forum:How to deal with contamination in bulkseq samples? Looking at correlated genes?

Question

[Seaweed]

Hi,

I have run a bulk RNA-seq for 4 tissue samples. Each sample contains 50 cells collected from FACS, but due to technical challenges, my cells of interest account for varying proportions of those 50 cells across the 4 preps. I am wondering if there are any ways to uncover genes that are expressed in my cells of interest even though the samples were a mixture of cell types. My cells are labeled by tdTomato, so I do have counts for tdTomato transcripts. One thought is to find genes that would correlate with tdTomato expression. Is this reasonable? If so, what would be a good way to look for correlated genes in the whole dataset? Clustered heatmap?

Thanks!