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


Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: