I need a suggestion from this wonderful community! I have data of 70 samples of two hypervariable regions: v3v4 and v4v5, sequenced in the same Miseq run
I analyzed the information separately and I obtained similar results from the two (yeahhh).
From a biological point of view, however, it is very difficult to discuss the data while keeping two regions. My idea is, therefore, to do an in silico PCR for the V4 and use the data of the counts of both.
The idea is to sum the V4 counts obtained for each sample starting from the assumption that the two observations are independent and therefore the result would be a representative proportion of the counts.
Do you think it makes sense? is there a batch effect that I’m not considering?
thank you so much for the possible suggestions and I hope you are all well