Is it possible to analyze data from barcode screens using DESeq2 (or a similar package, such as edgeR)?
More details: I have a library of barcoded knockout strains (much like an shRNA or CRISPR library) so that I can look for fitness differences as measured by strain count changes after exposure to the experimental condition. After growth in liquid culture, I took an aliquot of the strain as the input and treated several aliquots under my experimental conditions.
My understanding is that DESeq2 is more powerful when you have replicates of your control condition (e.g. 3 control vs 3 treated). However, in my case my control is the input "ground truth" of the prevalence of strains before treatment. I have several aliquots of the input, but they are derived from the same input sample. Would it be possible to consider these aliquots as different biological replicates for DESeq2 in order to power the analysis?
Another strategy I've seen is to use separate library inputs for each experimental replicate (so that you have e.g. 3 paired control-treated samples). Is there a way of telling DESeq2 to match these? Or would another analysis package be more appropriate to use in this case?