QIIME - Fungal 18S OTU picking, using BLAST
Download 18S reference database & decompresswget ftp://ftp.microbio.me/qiime/tutorial_files/its_12_11_otus.tgz tar -zxvf its_12_11_otus.tgz gzip -d its_12_11_otus/rep_set/97_otus.fasta.gz gzip -d its_12_11_otus/rep_set/99_otus.fasta.gz gzip -d its_12_11_otus/taxonomy/97_otu_taxonomy.txt.gz gzip -d its_12_11_otus/taxonomy/99_otu_taxonomy.txt.gz
# move folder "its_12_11_otus/" to a permanent database directory, accessible for example: /home/myname/data/its_12_11_otus/ Create OTU setting file > otu_18S_settings.txt echo "pick_otus:enable_rev_strand_match True" >> otu_18S_settings.txt echo "assign_taxonomy:assignment_method blast" >> otu_18S_settings.txt echo "assign_taxonomy:id_to_taxonomy_fp /home/myname/data/its_12_11_otus/taxonomy/97_otu_taxonomy.txt" >> otu_18S_settings.txt echo "assign_taxonomy:reference_seqs_fp /home/myname/data/its_12_11_otus/rep_set/97_otus.fasta" >> otu_18S_settings.txt # check content of parameter file
cat otu_18S_settings.txt pick_otus:enable_rev_strand_match True assign_taxonomy:assignment_method blast assign_taxonomy:id_to_taxonomy_fp /home/myname/data/its_12_11_otus/taxonomy/97_otu_taxonomy.txt assign_taxonomy:reference_seqs_fp /home/myname/data/its_12_11_otus/rep_set/97_otus.fasta export BLASTMAT=/home/myname/data/its_12_11_otus/rep_set/ # run OTU picking
pick_open_reference_otus.py -i seqs.fna -r /home/myname/data/its_12_11_otus/rep_set/97_otus.fasta -o
OTU_18S/ -p otu_18S_settings.txt --suppress_align_and_tree
# Result
biom convert -i OTU_18S/otu_table_mc2_w_tax.biom -o OTU_18S/otu_table_mc2_w_tax.tsv --to-tsv --header-key taxonomy
http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/Fungal-ITS-analysis.ipynb
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