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Mothur software analysis

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?

mothur 16s metagenome gut
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updated by Asaf Asaf • written by dpc dpc

1 answer

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.

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written by Asaf Asaf

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?

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written by dpc dpc

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

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written by Asaf Asaf

okay sir. thanks a lot for your kind suggestion.

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written by dpc dpc

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