I try to compare 8 samples that have been sequenced by the sequencing platforms Illumina MiSeq and Ion Torrent PGM. Samples that were sequenced by Illumina were further processed by the QIIME script pick_open_reference_otus.py (QIIME platform 1.9.1), Ion Torrent data was processed by Ion Reporter web platform for taxonomic annotation.
Now I would like to compare data after taxonomic annotation with the help of a Principal Coordinates Analysis (PCoA).
In general, is it possible to integrate Ion Torrent's data into the QIIME results so they can be further analysed together?
Ion Torrent produces fasta files for every sample on family and genus/species level. But I am completely unsure in which of the many result files in script's output folder these should be integrated for PCoA.
Another point is, that different taxonomic databases have been used (GreenGenes for QIIME, "Curated MicroSEQ(R)" and "Curated Greengenes" for Ion Reporter), which makes things further complicated.
So to sum up, is it possible at all to create a PCoA plot from data and which way would you recommend?
I already tried a lot of QIIME scripts, but without success. Any advice is really appreciated.