I followed the scrattch.hicat tutorial found here (https://taxonomy.shinyapps.io/scrattch_tutorial/#section-overview) with my scRNAseq dataset (instead of the tasic et al data) and the results says that my data has 6 clusters denoted by 6 different numbers (not 1-6). I looked up these numbers in the primary cell type id column of the Tasic, et al annotations file and identified the corresponding primary cell type. I thought, perhaps these cluster numbers are correlated to the Allen Brain cell types and these are my 6 cell types in my data! Then, I looked up these numbers in the Yao et al MOp mouse cortex data set annotations file, which revealed 6 different cell types. What does the user gain from these 6 cluster numbers if they are not correlated to an Allen Brain cell type? How does the user get to identifying “Vip Lmo1” or “Sst Cbln4” type of nomenclature for these 6 clusters? I do not see any output that gives the top 2 marker genes to be used for this naming convention. If it is possible I would like to classify my cell types the same way as the Allen Brain does so that way these cell types are comparable with the classified cell types published by Allen Brain. I completed the pipeline to get my 6 clusters by the same pipeline the Allen Brain folks use (scrattch.hicat) but I need help figuring out how I should name these 6 clusters to obtain nomenclature compatible with “Pvalb Tpbg”, etc.