mothur

Sub-sampled data

Hi, I have been following the following SOP workflow to work with 16s RNA gene sequences. According to the approach of my project I would like to find differences between groups and therefore I plan to use ANOVA.

My question is if I already subsampled the sequences in the mcc.shared file do I have to do it again (in terms of the relative abundance data, not sequences) to avoid sequencing depth errors or is the subsampling already implicit?

It is possible to get a single subsampled OTU table?

Thanks in advance

You can use the same sub-sampled count table to go into something like ANOVA. I doubt you really want to use ANOVA, however because your counts will not be normally distributed. Perhaps try lefse or metastats?

Pat

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