Merge otu tables from the denovo otu picking

Hi all,

I am very new to these analyses and I’m actually having problems when I want to combine the resulting OTU tables from two different datasets.

I am actually working with two different datasets (no shared samples and each sample with a unique ID) and I would like to know if there exists any command to merge the resulting OTU tables for each of the two datasets if I’ve performed denovo OTU picking. I cannot run both datasets at the same time because of memory and throughput limitations.

Up to now, I’ve only found potential solutions in case of having run reference-based OTU picking but as it is not my case, I do not know how to proceed.

Any idea or suggestion would be very appreciated.


You would have to start back at the beginning. OTUs are a product of the other sequences in the dataset. So adding information to the dataset may change the OTU structure.