I have completed the HiCAT tutorial for analyzing my 10x single-cell RNA sequencing data, but I am unclear about the need and purpose of comparing results with reference data. I would appreciate some clarity on the role of reference data in this analysis. If possible, could you also explain how to create reference data for a mouse brain in my case?
Additionally, once the iteration process is complete, I find that differential genes are sorted into numerous sections for all subclusters, creating hundreds of sections to review. I am contemplating skipping this step of comparison to concentrate on identifying marker genes for each cluster directly, especially if the creation of reference data is not possible.
Could you offer guidance or provide example code for analyzing my data without reference data? I am particularly interested in methods for identifying marker genes, visualizing clusters, and plotting a dendrogram.
Thank you