Final Aquarium Project data now ready!

Got the demultiplexed data back from all 4 Aquarium project runs, and now we’re going forward with OTU picking. Starting off with closed ref, to see what we get:

pick_closed_reference_otus.py -i /Users/hollybik/Desktop/Data/aquarium_project/All4MiseqRuns_demult_30Apr14/AQUEXP_all_MPF_2.fasta -o /Users/hollybik/Desktop/Data/aquarium_project/All4MiseqRuns_demult_30Apr14/uclust_closedref_30Apr14 -r /macqiime/greengenes/gg_13_8_otus/rep_set/97_otus.fasta -t /macqiime/greengenes/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt --parallel -O 2
Advertisements

Summarizing .biom table by sample name

This command collapsed replicates in the 18S_chimera .biom table, pooling all reads from the same sample site together:

summarize_otu_by_cat.py --otu_table_fp 18Schimera_openref99_20Oct13_otu_table_mc2_w_tax_metadata.biom --mapping_fp /Users/hollybik/Dropbox/Projects/18S_chimera/18S_chimera_mapping_qiime_format_remGOM_fungi15xR2.txt --mapping_category SampleName --output_fp 18Schimera_openref99_20Oct13_otu_table_mc2_w_tax_SampleName.biom

Note: I had to remove any samples that had zero representation in the .biom table (this included a couple of the GOM fungi replicates)