I have RNAseq data of cells sorted from mix cultures of 2 cell types as well as pure cell culture from only one of these 2 types. Read counts of certain transcripts specifically expressed in only one of the 2 cell types show that the sorted sample of one type always has a small amount of contamination from the other type, and vice versa. The contaminating read amounts vary from one replicate to another. Western blots confirm this contamination.
How do I normalize the transcript read counts for all other genes with this variable contamination? Does DESeq2, edgeR or any other software have a way to deal with this problem? If so, could you please point to the correct way of doing it?
Thank you very much!