Problem when retrieving biom file taxonomy


#1

Hi
I have a biom file that has several OTUs classified as
“id”:“Otu01218”, “metadata”:{“taxonomy”:[“Bacteria”, “Proteobacteria”, “Betaproteobacteria”, “Burkholderiales”, “Alcaligenaceae”, “Verticia”]

the problem is that MEGAN6 when importing the file places this branch as eukaryota,despite the fact that in mothur I removed all seqs classified as such, and eukaryota does not show in biom file.

Thanks for any help


#2

Please give me access to a small file that exhibits the problem and I will look into it.
D


#3

Hi Daniel
Sorry about the delay, was out of office and only now I was able to reply.
Here is the file.
Thank you for any help
Best
IgorTiago_4284B.trim.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.zip (227.6 KB)


#4

I first thought there might be some problem with a shared genus name with this guy:

But in fact, the NCBI taxonomy does not have the genus “Verticia” in “Alcaligenaceae” at all, only “Verticiella”, so this could be a problem with the taxonomy you used to classify the OTUs instead.