Yatsunenko data on QIIME

Of to a running start with the Yatsunenko et al. metadata!  Got the files passed on from Guillaume and organized

Mapping files are as follows

  • qiime_ps_metagenomes_mappingfile.txt (16S pulled down from PhyloSift runs
  • qiime_16S_amplicon_mappingfile.txt (16S amplicons from the broad rRNA sequencing, pruned to 107 we have metagenomes for)

Yatsunenko et al. metagenome data commands as follows (following the commands listed in the paper itself, closed-ref picking at 97% against greengenes 97% condensed database):

cat  *.fna >> ps_metagenome_combined.fna

pick_otus.py -i /home/ubuntu/data_yatsunenko/ps_metagenome_extract/ps_metagenome_combined.fna  -m uclust_ref -r /home/ubuntu/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -o /home/ubuntu/data_yatsunenko/ps_metagenome_extract/uclust_ref_97_ps_metagenomes -s 0.97 –max_accepts 1 –max_rejects 8 –stepwords 8 –word_length 8

cd /home/ubuntu/data_yatsunenko/ps_metagenome_extract/uclust_ref_97_ps_metagenomes

pick_rep_set.py -i s_metagenome_combined_otus.txt -f /home/ubuntu/data_yatsunenko/ps_metagenome_extract/ps_metagenome_combined.fna -r /home/ubuntu/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -o ps_metagenomes_rep_set.txt

assign_taxonomy.py -i ps_metagenome_rep_set.txt -r ~/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -t ~/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt

align_seqs.py -i ps_metagenome_rep_set.txt -t ~/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011_aligned.fasta -m pynast -o pynast_aligned/

Played around more with lots of stuff and sorted out parameter and mapping files for the core analyses. Running a test on the ps_metagenome data, as follows:

core_qiime_analyses.py -i /home/ubuntu/data_yatsunenko/ps_metagenome_extract/ps_metagenome_combined.fna -o /home/ubuntu/ps_metagenome_coreanalyses_14sept -m qiime_ps_metagenomes_mappingfile.txt -f –suppress_split_libraries -t /home/ubuntu/gg_otus_4feb2011/trees/gg_97_otus_4feb2011.tre -p /home/ubuntu/qiime_parameters_ps_amplicon.txt


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