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Most of the steps for analysis of 18S, or mixed 16S/18S, are identical to the standard 16S pipeline described in the QIIME Illumina Overview Tutorial or the QIIME 454 Overview Tutorial, with the main difference being the use of a non-default reference database. Alternative QIIME-compatible reference databases can be found on the QIIME resources page. Please refer to the Fungal ITS Analysis Tutorial for an example of how to perform a QIIME analysis with a non-default reference database.
It may be desirable to split the OTU table according to domain for mixed 16S/18S datasets. To do this, you can use split_otu_table_by_taxonomy.py to split at the domain level (2):
split_otu_table_by_taxonomy.py -i otu_table.biom -L 2 -o split_otu_tables/
The output directory, split_otu_tables, will contain an OTU table for archaea, bacteria, and eukaryotes, which can be utilized in downstream QIIME analyses.