I'm very new to scRNA-seq data so I'm sorry if I eventually posed a trifling question. I orchestrated a sc-cell experiment passing through several steps. First of all I eliminated all the genes that are not expressed in any cells. After this I managed to implement QC to remove poor quality cells. I normalized the survival cells clustering them by the procedure suggested with the scran package (Lun, 2019) and then i ran tSNE to have a 2D map using the previous found clusters to get an idea of the cells in my dataset. My question is, by your experience what procedure would you suggest to me in order to infer what kind of tumour cells compose each cluster?
I'm dealing with findMarkers function that by following functions provides the possibility to see which genes characterises the more one cluster with respect to the others, plotting some useful heatmaps. Given that I have 15 clusters is it good to repeat this procedure for each cluster?Is there a more time preserving and technical strategy that would you recommend to me? I feel very naive to proceed like I told you. Thank you in advance