Hello, I am a student doing a project with some conceptual difficulties (I do realise such question optimally shouldn't occur). The project aims to compare 8 RNA-seq samples (4 vs 4) testing for differentially expressed genes. The problem is that 2 of the samples (1 for each categories) weren’t amplified as much as the others (an additional 5 cycles).
Obviously, such treatment is sub-optimal for comparative studies, I was wondering what was the best remedy for this problem short of resequencing. I was considering DESEQ2 for it’s outlier capacities or dropping the samples (doing a 3 vs 3) Additional information: the transcriptome is de novo using the samples.