I have recently received results from a microbiota analysis conducted by 300bp paired-end read (Illumina MiSeq) on faecal samples.
The information delivered contains lot of data such as 16S pre-processing and OTU picking, OTU diversity analyses with QIIME and so on. I am not very familiar with these kind of data since I have usually worked with relative abundances of taxa from 454 pyrosequencing results.
So, I would really much appreciate your help with the following question:
In order to conduct statistical analyses, do I have to take into consideration the OTU count table (OTUs count for each of the analysed samples) or do I also have to take into account other information provided such as the OTU consensus taxonomy summary, sequence taxonomy summary...?
Thank you very much in advance for your help,