GOM data analysis – yet more QIIME

Continuing next steps with QIIME. Filtering alignments next:

filter_alignment.py -i /home/ubuntu/GOM_demulti2_rev_OpenRef_uclust99_12Oct/aligned_seqs/GOM_concat_rev_d
emultirepeat_1to12_2_otus_rep_set_aligned.fasta -o /home/ubuntu/GOM_demulti2_rev_OpenRef_uclust99_12Oct/aligned_seqs/GOM_concat_rev_
demultirepeat_1to12_2_otus_rep_set_filtered_aligned.fasta -s -e 0.10 -g 0.90

filter_alignment.py -i /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/aligned_seqs/GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set_aligned.fasta -o /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/aligned_seqs/GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set_filtered_aligned.fasta -s -e 0.10 -g 0.90

Now assigning taxonomy:

parallel_assign_taxonomy_rdp.py -i /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/GOM_concat_fwd_demultirepeat_1to12_1_otus_rep_set.fasta -r /home/ubuntu/Silva_108/rep_set/Silva_108_rep_set_Eukarya_only.fna -t /home/ubuntu/Silva_108/taxa_mapping/Silva_RDP_taxa_mapping_Eukarya_only_species.txt -o /home/ubuntu/GOM_demulti2_fwd_OpenRef_uclust99_12Oct/rdp_taxonomy/ -c 0.7 -O 6

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