Mothur software analysis

Question

[dpc]

Hi friends!!! I am analysing data with MOTHUR software. I've gone through the MiSeq SOP. But still I have one confusion. Should I analysis the "control" and the "test" data separately or mix together and analyse at once? I am asking this as i have analysed separately but stucked at the statistical step. Any idea?

Answer 1

[Asaf]

You should analyze everything together so the OTUs will be the same. At the end of the process you will have a count table that will include all of the samples and then you could conduct a comparative analysis.

[dpc]

Thank you sir for your fast response. One more query. If I analyse separately, somehow can I merge them and do PCOA and heatmap study?

[Asaf]

No, you'll have to run it again. That's a known downside of mothur, methods like dada2 or deblur do allow this.

[dpc]

okay sir. thanks a lot for your kind suggestion.