We have a cell line with certain plasmids added. The initial sample was split into three subsamples, plus it was sequenced once. The three subsamples were grown differently, then each sequenced once (of course the four library was pooled begore sequencing with their respective barcodes added). The sequencing only happened of one part of the plasmids, where there was a 30 nucleotide long variable region with >100000 variants. We would like to compare the number of respective variants between the initial sample and the subsamples.
My questions: how would you normalize this data to get the change ratio of each variant?
I hope it's clear, please tell me if not, I would edit thr question.
EDIT: It may sound somewhat similar to a differential expression analysis, however, we only expect the variants to be cut, there are no 'upregulation' in this case.