Hello! I’m new to the field of single-cell RNA sequencing, and I need to analyze some datasets consisting of 10 samples across 2 different conditions. I’m facing challenges in the cell type classification step because my data are derived from cerebrospinal fluid (CSF), whereas the canonical reference-based classification models are trained on blood-derived data. I’m considering using marker-based methods like cellAssign, but this requires obtaining marker genes for each cell type from the literature. However, after an extensive search, I’ve found that there isn’t a strong consensus on the most important markers for accurately defining every cellular type. Therefore, I have the following questions:

1. Is CSF similar to blood, and can I simply use reference-based models in my situation?
2. If not, how can I achieve correct cell type classification?

Thank you a lot