I am new to single cell RNA-Seq, and am trying to find a workflow related question. I have aligned about 1500 cells from two different experiments (but using same experimental procedure). I am wondering how do I go ahead with differential expression analysis. Should I merge all the bam files and then generate a count table? or should I use string tie on each cell (use the hisat-stringtie pipeline). I am a bit confused because the data set is too large. I understand that ultimately I should have an expression matrix (Genes/Expression level/cell). What should be the next step after alignment (i,e creation of individual bam files) ? Please advice.