Yatsunenko and GOM – more QIIMEing

Continuing where I left off with the QIIME analyses. For the Yatsunenko data, trying to finish up the 16S amplicon analyses before the sprint ends on Friday (have to do this manually because the core analyses workflow just wasn’t working for the huge dataset):

pick_rep_set.py -i /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/16S_amplicon_yatsunenko_combo_otus.txt -m first -o 16S_amplicon_yatsunenko_combo_otus_rep_set.txt -s otu -r /home/ubuntu/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta

align_seqs.py -i /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/ 16S_amplicon_yatsunenko_combo_otus_rep_set.txt -t /home/ubuntu/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011_aligned.fasta -m pynast -a uclust -o /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/aligned_seqs/ -e 150 -p 0.75

filter_alignment.py -i /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/aligned_seqs/ 16S_amplicon_yatsunenko_combo_otus_rep_set_aligned.fasta -o /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/aligned_seqs/ -g 0.999999 -t 3.0 –suppress_lane_mask_filter

assign_taxonomy.py -i /home/ubun
tu/ps_16Samplicons_parallel_picktotus_17sept/16S_amplicon_yatsunenko_combo_otus_rep_set.txt -t /home/
ubuntu/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt -r /home/ubuntu/gg_otus_4feb2011/rep_
set/gg_97_otus_4feb2011.fasta -m rdp -c 0.8 -o /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept
/assign_taxonomy/

make_otu_table.py -i /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/16S_amplicon_yatsunenko_combo_otus.txt -o /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/ 16S_amplicon_yatsunenko_combo_otu_table.biom -t /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/assign_taxonomy/ 16S_amplicon_yatsunenko_combo_otus_rep_set_tax_assignments.txt

beta_diversity_through_plots.py -i 16S_amplicon_yatsunenko_combo_otu_table.biom -m /home/ubuntu/qiime_16S_amplicon_mappingfile.txt -o /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/beta_diversity/ -t /home/ubuntu/ps_16Samplicons_parallel_picktotus_17sept/aligned_seqs/ 16S_amplicon_yatsunenko_combo_otus_rep_set_aligned_pfiltered.tre -p /home/ubuntu/qiime_parameters_ps_amplicon.txt

And for the GOM Data, proceeding manually (core analyses ran into an error at the RDP step). Commands as follows:

align_seqs.py -i /home/ubuntu/uclust_99_GOMillumina_fwd_1to12_1/otus/rep_set/ GOM_illumina_demultiplexed_fwd_concat_1to12_1_rep_set.fasta -t /home/ubuntu/Silva_108/core_aligned/Silva_108_core_aligned_seqs.fasta -m pynast -a uclust -o /home/ubuntu/uclust_99_GOMillumina_fwd_1to12_1/otus/aligned_seqs/ -e 150 -p 0.75

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