I am analyzing data generated using the indrop protocol (https://www.nature.com/nprot/journal/v12/n1/full/nprot.2016.154.html). There are 4 samples that were sequenced and each sample roughly has about 1500 cells. I've performed all the preprocessing steps and using Seurat did the cluster analysis. I've about 6 cluster and using Seurat(FindAllMarkers) identified important gene markers for each of the clusters. What steps/tests should be performed in order to compare these gene markers across all the 4 samples? For example, if I am interested in GeneA, would it make sense just to compare total expression of GeneA in all the 4 samples? or are there statistical tests that could be used to do this? Hope this question makes sense. Also, What mitochondrial abundance is normally seen per cell while analyzing any type of sc-RNA data? I understand this is a prep dependent question but anything from your experience might be useful.