Re-training the RDP Classifier¶

Retraining the RDP classifier and assign taxonomy¶

This tutorial covers how to retrain the RDP Classifier with an alternate taxonomy to use the RDP Classifier with arbitrary taxonomies. This is useful, for example, to assign greengenes taxonomy strings to your sequences, or to assign taxonomy to eukaryotic sequences using the Silva database.

This tutorial will illustrate an example where you’ve run the QIIME Overview Tutorial, and then want to re-assign taxonomy using the greengenes taxonomy. To do this you’ll need the greengenes reference OTUs. This is covered in the first step.

This tutorial assumes that you’ve already run the QIIME Overview Tutorial, and that you’re working in the directory where you ran the tutorial commands.

Getting the greengenes reference OTUs¶

The most recent version of the greengenes OTUs is always listed on the top right corner of the QIIME Blog homepage (click the “Most recent Greengenes OTUs” link on that page). As of this writing that is the 4feb2011 version, so we’ll illustrate commands working with that.

Download and unzip the greengenes reference OTUs:

wget http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/Caporaso_Reference_OTUs/gg_otus_4feb2011.tgz
tar -xvzf gg_otus_4feb2011.tgz

Re-train the RDP Classifier and classify the representative sequences¶

Next you’ll retrain the RDP classifier and classify your sequences. You can use either assign_taxonomy.py or parallel_assign_taxonomy_rdp.py for this.

assign_taxonomy.py -i otus/rep_set/seqs_rep_set.fasta -t gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt -r gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -o otus/rdp_assigned_taxonomy_gg/

Integrate the taxonomy assignments into a new OTU table¶

Next, you’ll rebuild the OTU table with the new taxonomic information.

make_otu_table.py -i otus/uclust_picked_otus/seqs_otus.txt -t otus/rdp_assigned_taxonomy_gg/seqs_rep_set_tax_assignments.txt -o otus/otu_table_gg.txt

That’s it. The resulting OTU table (otu_table_gg.txt) can now be used in downstream analyses, such as summarize_taxa_through_plots.py.

Retraining RDP using a custom parameters file¶

If you want to integrate retraining of the RDP classifier into your QIIME workflows, you can create a custom parameters file that can be used with the pick_otus_through_otu_table.py workflow script. If the gg_otus_4feb2011 directory is in /home/qiime/, the values in your custom parameters file would be:

assign_taxonomy:reference_seqs_fp       /home/qiime/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta
assign_taxonomy:id_to_taxonomy_fp       /home/qiime/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt

Defining alternate training files¶

Training files can be defined by users for other taxonomies. The format is the same as the id_to_taxonomy_map used by the BLAST taxonomy assigner, defined here. You must provide this file as well as a fasta file of reference sequences where the identifiers correspond to the ids in the id_to_taxonomy_map.

The RDP Classifier has several requirements about its taxonomy strings for retraining. The first entry in each taxonomy string must be Root, and there must be exactly six levels, including Root. For example, the first four lines in the 4feb2011 greengenes OTUs are:

573145  Root;k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae
89440   Root;k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae
452783  Root;k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae
430240  Root;k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae

Re-training the RDP Classifier¶