Hi everyone,
I’m asking a stupid question. Do you guys know where can I find out the OTUs for each sample? Like a list to show me how many OTUs in sample1 and sample 2, 3, 4, 5,6 and what OTUs are shared with all the samples (which OTU is unique). I went through the MIseq SOP but did not find this kind of output from mothur. I collected samples at 6 time points from a single animal and would like to know how the diversity changes. any suggestions or comments are greatly appreciated and thanks,
Jinxin
This would be in the shared file generated by make.shared.
thank you very much Dr. Schloss. I found all the OTUs for each sample from the shared file but I got another question. There is only 188 OTUs are found in all these samples (from the shared file). However, when I looked at the classify.OTU output and I had 27780 OTUs in total and I still have 6998 OTUs after removing singletons. I don’t understand why these numbers dropped down to only 188 (from 27780)? I’m guessing that’s the cutoff (0.03) made the change? But I mean that’s a huge difference and I don’t know which OTU numbers are correct. Can you please explain me a little bit how the cutoff will work at this point? I really appreciate your time and help. thanks,
Jinxin
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thanks, but can you please answer my questions? I still don’t understand why the numbers dropped to only 188 OTUs? Any differences between the make.shared output and classify.OTU output, I mean for these OTUs?
The 188 likely represents OTUs where all samples are present, and the remaining non-singleton contain a subset of the samples. Mothur has two commands to help you find the OTUs that are unique and shared by different samples. The venn command, http://www.mothur.org/wiki/Venn, and the get.sharedseqs command, http://www.mothur.org/wiki/Get.sharedseqs. The get.sharedseqs command allows for more specific settings for the samples whether you are looking for “unique to” or “shared by” options. You will want to pay close attention to the uniquegroups and sharedgroups options.