Hello all,
I have download two scRNAseq experiments from two different studies. After creating the seurat file using (features, matrix, counts), I removed the doublets, normalize these two samples using harmony and, in general, the result is pretty decent.
However, there are some very distinct clusters only present in one of the samples. When I check which specific markers they have, they are all mainly unspecific genes. In addition, these genes are expressed in all the cells of only one sample, independently of the UMAP cluster. this indicates that these genes are only counted/called in one of the studies, I guess.
Do you have any thoughts about this? I guess there is a method to filter all genes that are not present in all the studies to a certain level, as we can do in bulk rnaseq, but I don´t know how to do it in scRNAseq.
Thanks, Robert
