I used to use Qiime for 454 sequences and when one was through, one could look for sequence OTU identifiers in one of the sequence file headers if one wanted to pull specific sequences for further identification (say, down to species level). Now I am using Qiime for Illumina data and can't find a similar cross-reference. Is this possible with this data? I can find the OTU identifiers and correlate them with a specific genus, but cannot find an fna file that has both the OTU identifier and the specific sequences that correspond to the identifier. I desperately need to be able to pull sequences belonging to specific genera and don't want to use BLAST (for obvious reasons), especially as the work has already been done.
Assuming you performed the default closed reference OTU picking protocol in QIIME, the reference fasta file would be from Greengenes, preclustered at 97% similarity. The actual file name would be 97_otus.fasta, and you should be able to find it within your QIIME installation folder. The OTU ids correspond to sequence names in this file. If you have a list of OTU Ids, you can then use the filter_fasta.py command in QIIME to pull the corresponding sequences.
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