I am integrating 4-5 datasets, all belonging to mouse. One of the datasets has a gene, “eGFP”, which is not present in other datasets. By the term “not present”, I mean to say that only one of the datasets was aligned with genome containing eGFP as a gene while other datasets have been aligned with a different genome (which doesn’t contain eGFP even though it has all the other genes from mus musculus assembly).
Is there a way I could retain this gene while integrating? Intuitively, I would like to just define a new gene “eGFP” in other datasets and keep its count value to zero for all the cells. However, I am not sure how to define a new gene ?