I am trying to analyze some single cell RNA seq data. I have two samples. One is from a wild type spleen and the other spleen has a gene knockout. I have some questions regarding the analysis.
From going through Seurat tutorials it seems like I would have to integrate the 2 samples. Should I first load the 2 datasets in seurat, do the QC analysis, normalize,
FindVariableFeaturesand then select the features for integration and integrate? Would it be appropriate to merge them first for the QC analysis? On the seurat tutorial for merging it says to normalize and identify variable features for each dataset independently so would merging the datasets cause an issue?
FeaturePlotfor the knockout gene be more appropriate to show that the knock out was successful?
I would like to do differential gene expression analysis to compare one cell type between wild type and knockout. Would it be better to use the
FindMarkersfunctions in Seurat using the MAST test or would it be better to use pseudobulk?