I'm going to detect differentially expressed genes with RNA-seq data got from some "GFP positive cells" and "GFP negative cells". However, the cDNA are sequenced with two different methods, one as "normal" RNA-seq, and the other is low-input RNA-seq (only requires a small amount of starting materials). Here's the summary of number of dataset I got in each cell type with each method:
GFP positive cells * normal RNA-seq : 1
GFP negative cells * normal RNA-seq : 1
GFP positive cells * low-input RNA-seq : 3
GFP negative cells * low-input RNA-seq : 2
In such a case, what kind of statistics/tools can be applied to detect DEGs in GFP positive cells VS GFP negative cells?