I need some help in deciding the tools and steps in the following analyses. I got 6 RNAseq samples, there are no replicates among the six samples. These six samples are from three different tissues. Three of them are wild-type (WT) samples and the remaining three of them are knock-out (KO) samples.
I checked with the coordinator, they don't have any replicates for the 6 samples. But he also mentioned that tissue1 and tissue2 are somewhat similar.
I have used the following tools for this pairwise analysis
a) Tissue1_WT and Tissue2_WT vs Tissue1_KO and Tissue2_KO (i.e Tissue1_WT is replicate1 and Tissue2_WT is replicate2 for WT and similarly Tissue1_KO is replicate1 and Tissue2_KO is replicate2 for KO groups).
step 1) Trimmed using Trimmomatic
step 2) Aligned using HiSAT2
step 3) HTSeq count from the BAM files
step 4) Differential gene expression analysis using DESeq2
Steps 1-3 are the same for the below pair-wise analyses, but can I still use DESeq2 for samples without replicates?
2) Tissue1_WT vs Tissue1_KO
3) Tissue2_WT vs Tissue2_KO
4) Tissue3_WT vs Tissue3_KO
Any suggestions are appreciated.