Yatsunenko more analysis yay

Getting more analyses done in prep for the paper. We wanted to know what taxa were causing the PCoA groupings across components. QIIME forum suggested we do bi-plots for this. Summarized OTU table and then made the plot (in home/hollybik/yatsunenko_QIIME/ps_16Samplicons_parallel_picktotus_17sept/beta_diversity/biplots on Edhar):

summarize_taxa.py -i 16S_amplicon_yatsunenko_combo_otu_table.biom -L 6 -o summarize_taxa/

make_3d_plots.py -i weighted_unifrac_pc.txt -m /home/ubuntu/qiime_16S_amplicon_mappingfile.txt -t /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/summarize_taxa/ 16S_amplicon_yatsunenko_combo_otu_table_L6.txt -o biplots/

Also ran alpha diversity metrics – this command wasn’t working before, but all seemed to be OK the second time I tried running it on the 16S amplicon data.

alpha_diversity.py -i 16S_amplicon_yatsunenko_combo_otu_table.biom -o /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/alpha_diversity -t /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/aligned_seqs/ 16S_amplicon_yatsunenko_combo_otus_rep_set_aligned_pfiltered.tre


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