pick_open_reference_otus.py outputs and make_otu_table.py

[Beatriz Gil Pulido]

Hi, 

I am user of QIIME1 as my latest analyses were run with that version. I am running the data using SILVA_128 instead of SILVA_123 and see if there are significant differences. I always use pick_open_references_otus.py. 

My workflow was as follows: 

1)pick_open_reference_otus.py -i usearch_checked_chimeras/seqs_chimeras_filtered.fna -r SILVA_123_rep_set97_16s_only.fna -m usearch61 --suppress_taxonomy_assignment -o otus 

Since I suppressed the taxonomy, I additionally ran the following commands: 

2)assign_taxonomy.py -i otus/rep_set.fna -r SILVA_123_rep_set97_16s_only.fna -t SILVA_123_taxonomy_97_7_levels_16s_only.txt -o assigned_taxonomy

3)make_otu_table.py -i otus/final_otu_map_mc2.txt -t assigned_taxonomy/rep_set_tax_assignments.txt -e otus/rep_set_failures.fasta -o otus/otu_table.biom

4)summarize_taxa_through_plots.py -i otus/otu_table.biom -m mapping_file_all_R3_reverse.txt -s -o taxa_summary

This time, using SILVA_128, I cannot proceed in that way since in the output from assign_taxonomy.py I don't get the rep_set_tax_assignments.txt file that it is required for make_otu_table.py. 

Instead, I am running the pick_open_reference_otus.py without suppressing the taxonomy. In that case, within the -o otus appears a folder "unclust_assigned_taxonomy" where I can find the rep_set_tax_assignments.txt neccesary to proceed from 3). However, I am wondering if otu_table_mc2_w_tax.biom output (when not suppressing taxonomy from 1) ) is already the otu_table I might use for next steps like summarize_taxa_through_plots.py or for alpha and beta diversity scripts. 

Now I am feeling pretty much confused because:

A) I don't know if after running script 1) I have to use final_otu_map_mc2.txt to go to 2) 

B) if it is necessary to go to 2) using final_otu_map_mc2.txt or instead if otu_table_mc2.biom would be the otu_table.biom I have to use for summarize_taxa_through_plots.py and diversity scripts

C) if otu_table_mc2_w_tax.biom is the biom table I have to use for all my analysis if --suppress_taxonomy_assignment isn't ran. 

I would really appreciate some help with it as I have already ran different options and I am very confused. 

Regards, 

Beatriz.