GOM Illumina – next steps with QIIME

Getting back to GOM data analysis on the Amazon cloud. I had run the fwd OTU picking too but forgot to note down the command (finished on Oct 16th):

pick_otus.py -i ~/GOM_demultiplexed/GOM_concat_fwd_demultirepeat_1to12_1.fna -m uclust_ref -o /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct -r /home/ubuntu/Silva_108/rep_set/Silva_108_rep_set_Eukarya_only.fna -s 0.99 –enable_rev_strand_match

Proceeding with picking rep set of sequences:

pick_rep_set.py -i GOM_concat_fwd_demultirepeat_1to12_1_otus.txt -f ~/GOM_demultiplexed/GOM_concat_fwd_demultirepeat_1to12_1.fna -m first -l pick_rep_set.log -o GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set.fasta

pick_rep_set.py -i GOM_concat_rev_demultirepeat_1to12_2_otus.txt -f ~/GOM_demultiplexed/GOM_concat_rev_demultirepeat_1to1
2_2.fna -m first -l pick_rep_set.log -o GOM_concat_rev_demultirepeat_1to12_2_otus_rep_set.fasta

Next need to align sequences:

parallel_align_seqs_pynast.py -i /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set.fasta -t /home/ubuntu/Silva_108/core_aligned/Silva_108_core_aligned_seqs.fasta -a uclust -o /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/aligned_seqs/ -e 70 -O 6

parallel_align_seqs_pynast.py -i /home/ubuntu/GOM_demulti2_rev_OpenRef_uclust99_12Oct/GOM_concat_rev_demultirepeat_1to12_2_otus_rep_set.fasta -t /home/ubuntu/Silva_108/core_aligned/Silva_108_core_aligned_seqs.fasta -a uclust -o /home/ubuntu/GOM_demulti2_rev_OpenRef_uclust99_12Oct/aligned_seqs/ -e 70 -O 6

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