Closed OTU analysis from provided biom

[black.beaker]

Hi All,

I am relatively new to this pipeline so please forgive any obvious questions.

I have currently imported (and converted) a .biom file (closed data) and mapping file I have been provided for analysis. However, I am a little stuck at the point of generating the rep-seqs.qza and was wondering if anyone can clarify for me if, for closed OTU data, this is just a conversion of aligned 97% OTUs reference sequences from greengenes and use of fasttree to make the phylogenetic tree for later analysis, or is there something I am missing that I need to ask our collaborator to provide?

Any help (or pointing in direction of useful link) greatly appreciated

Cheers

[ebolyen (Evan Bolyen)]

Hi @black.beaker,

@black.beaker

However, I am a little stuck at the point of generating the rep-seqs.qza and was wondering if anyone can clarify for me if, for closed OTU data, this is just a conversion of aligned 97% OTUs reference sequences from greengenes and use of fasttree to make the phylogenetic tree for later analysis, or is there something I am missing that I need to ask our collaborator to provide?

You are exactly right, you should just import the reference sequences from your closed-reference database of choice and use that new artifact for anything that might need them. You should also do the same for your phylogeny (fasttree+mafft is only needed if you don't already know the phylogeny).

Check out this section of the Importing tutorial for examples. For the Phylogeny, just change it from Phylogeny[Unrooted] to Phylogeny[Rooted].

Let me know if you run into issues!