I am new to microbiome processing pipeline but I want to ask, How do I combine two observations and assign it to a new single observation in the OTU table resulted from QIIME.
Here is the situation. I am doing river microbiome analysis. I have water sample named A-P, P for particle-attached sample and A for its and A-F for free-living sample for the same site. They are just different in the filter size being used.
I extracted the DNA, sequenced, and processed the raw reads separately using QIIME for all the 110 samples. But now, I am doing analysis on "R" and i need to combine A-F and A-P as one observation, namely only A. It seems simple to do on "R" for only one observation. But, I have 110 observations needed to be merged to 55. Are there any simple ways doing that without doing it one by one either in "R" or QIIME
Thanks, Bob Adyari