I have RNAseq data from 4 samples with 3 biological replicates per sample. I am currently trying to do the differential expression analysis with DESeq2 but the biological replicates will not cluster together when I make the PCA plot or correlation heatmap. This is my first time with RNASeq analysis and so am not sure what the best route forward is? I would like to avoid repeating the experiment with new samples if possible!
My pipeline prior to DESeq2 was the following:
FastQC quality check -> Trimmomatic -> Kallisto
I used tximport to convert kallisto files into suitable format for DESeq2