Getting started with Aquarium Project data

The data is in – time to get started in QIIME! Walked David through some workflows, but then executed my own reference-based OTU picking as a first pass through the data. Note: 4 parallel OTU picking jobs was too much for my iMac – suggest dropping this to 2 jobs next time so my computer doesn’t slow to a crawl.

Commands I ran:

parallel_pick_otus_uclust_ref.py -i /Users/hollybik/Desktop/Data/aquarium_project/demul_trim_prep_noBCmismatches/input_data/AQUEXP1.MPF.all_reads_merged_30May.faa -o ~/Desktop/Data/aquarium_project/demul_trim_prep_noBCmismatches/uclust_ref -r /macqiime/greengenes/gg_12_10_otus/rep_set/99_otus.fasta -O 4 −−enable_rev_strand_match
 
pick_rep_set.py -i /Users/hollybik/Desktop/Data/aquarium_project/demul_trim_prep_noBCmismatches/uclust_ref/AQUEXP1.MPF.all_reads_merged_30May_otus.txt -r /macqiime/greengenes/gg_12_10_otus/rep_set/99_otus.fasta -l pick_rep_set.log
 
assign_taxonomy.py -i /Users/hollybik/Desktop/Data/aquarium_project/demul_trim_prep_noBCmismatches/uclust_ref/AQUEXP1.MPF.all_read_merged_30May_rep_set.fasta -m rdp -r /macqiime/greengenes/gg_12_10_otus/rep_set/99_otus.fasta -t /macqiime/greengenes/gg_12_10_otus/taxonomy/99_otu_taxonomy.txt
 
make_otu_table.py -i /Users/hollybik/Desktop/Data/aquarium_project/demul_trim_prep_noBCmismatches/uclust_ref/AQUEXP1.MPF.all_reads_merged_30May_otus.txt -o AQUEXP1.MPF.all_reads_merged_30May_otu_table.biom -t /Users/hollybik/Desktop/Data/aquarium_project/demul_trim_prep_noBCmismatches/uclust_ref/rdp_assigned_taxonomy/AQUEXP1.MPF.all_read_merged_30May_rep_set_tax_assignments.txt
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