Hello researcher and developer @fbeghini.
It’s my first time to analyse shotgun and I have difficulties to communicate metaphlan output to phyloseq.
I have used merge_metaphlan_tables.py but in absolute counts (code available from https://forum.biobakery.org/t/merge-metaphlan-tables-py-with-absolute-abundance/1839) but when I tried to construct the otu table I obtained the following output:
I have all the taxonomic ranks mixed in the first column. Therefore, I understand that I cannot do tax_glomf function in phyloseq R package.
Therefore it will be interesting to construct 7 independent OTU tables (one for each taxonomic rank) and construct 7 phyloseq objects?
Thanks for your help,
Kind regards,
Magí.