I have RNA-seq .bam files for 3 patients, tumour and its matched derived model, namely organoid, but I don't have any matched normal sample.
Differentially expressed genes between a tumour and its model mainly come from the presence and lack of microenvironment in cancers and organoids respectively and response to stimuli (artificial environment in organoid culture vs cancer.
How I can get the differentially expressed genes specific to microenvironment?
Any intuition please?