I have a single cell dataset and based on reference dataset I expect about 40 clusters. I did try to use a cluster evaluation tools (scclusteval) and the combination of parameter it recommends which gives optimum number of stable clusters results in less than 30 clusters. Now, my questions. are
How much it is necessary to do the cluster evaluation? it really takes my time as it's a bootstrapping method. should I be worried if I don't do it I cannot trust my result?
Second, as it does not result in 40 clusters as a reference dataset I need to do subclustering which is another step. I am wondering which one do you recommend more? to do reclustering or not using the tool and increase the resolution to get the number of clusters I'm looking for?
Thank you for your help in advance!