I am about to start my journey with microbiome analysis. I got sequencing results from Eurofins. It contains several files and I am not sure if I understand them correctly.
I've tried to check out alpha- and beta-diversity, but at some point I stuck with plugin error from diversity:
The table does not appear to be completely represented by the phylogeny.
And now I am wondering if I used a proper files to start analysis. Therefore, I share the description of files which I got from Eurofins:
I though that I can import .biom file and use it as table with feature counts. Then I used 03_OTU_representative_sequences.fasta to do a rooted tree and I got a tree like this:
...but it does not make any sense. I want to perform microbiome analysis with my metadata collected from patients. Thus, which file should I use to get a proper Feature Counts?
Thank you for every tip and sorry for stupid questions...
In the spirit of transparency, I have not worked with Eurofins data, nor can I find much on their webpage. Based on the description, I would use the out_table.biom and the OTU_representative_sequences.fasta as my starting place from their outputs. The tree tip problem has come up a few times, you might want to look at some of the threads I'll link at the bottom.
That said... if it were my data, I'd start over and denoise the data myself. You get higher resolution features and you know exactly how the data was processed bioinformatically.
forum!