Can anyone advise me if the biom file generated in mothur from .shared (having used the greengenes 13_8_99 database for classify.seqs) b merged wiht biom files generated in OTU picking scripts in QIIME (as open_reference_otu_picking.py), which by default uses the 13_8_99 alignment for its OTU picking, as i understand? I tried the merge_otu_tables.py script from QIIME to do this, but it delivered a number of formating errors, i think.
The reason i ask this is if someone wants to combine taxonomic data extracted from metagenomic datasets in QIIME or say metaphlan and 16S datasets analysed in mothur, how can it be done? Or can it be done at all?
If anyone has any suggestions or similar experiences, please advise.