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

  • $\begingroup$ There is no word "wanna" in English. I have changed it to "want to" in your question. $\endgroup$ – David May 11 '18 at 16:46
  • $\begingroup$ Which is the output you are working on from QIIME? is it biom-format? $\endgroup$ – aLbAc May 22 '18 at 15:49
  • $\begingroup$ sorry for the long missing. I figured it out already in a bit complicated way. So, I ran collapse_samples.py in qiime to merge two samples to one new. Thanks anyway $\endgroup$ – Bob Adyari Jun 12 '18 at 9:16

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