I have analysed 50 16S amplicon datasets using the v3-v4 regions (PE, 250 bp, merged, and ~450 bp merged reads formed) and generated an OTU table. Suddenly, we have recieved another 10 samples that were sequenced individually for v3 (PE, 300 bp) and v4 (PE, 300 bp) regions. Is there a way to merge/join these two individual datasets before calling OTUs for all 60 samples using v3-v4?
I am trying to avoid trimming v3 or v4 parts from the large datasets to make individual v3 and v4 datasets and then caling OTUs separately using v3 and v4 regions.
Any suggestions or ideas would be apprecited.