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bash_vsearch_ecotag
bash_vsearch_ecotag
Commit 3b8e72cb authored by peguerin's avatar peguerin
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correct path

parent 822454f4
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main.sh
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......@@ -54,12 +54,12 @@ obitab -o $all_sample_sequences_sort > final/all.csv
## Assign each sequence to a taxon according to alternative SPYGEN fasta sequences
spygen_bdr_fasta="/donnees/rhone_all/teleo_V1_0_VM.fasta"
all_sample_sequences_tag-spygen="${dereplicated_all/.fasta/.tag-spygen.fasta}"
ecotag -d "$REF_DATABASE"/"${base_pref}" -R "$spygen_bdr_fasta" $dereplicated_all > $all_sample_sequences_tag-spygen
spygen_bdr_fasta="/media/superdisk/edna/donnees/rhone_all/teleo_V1_0_VM.fasta"
all_sample_sequences_tag_spygen="${dereplicated_all/.fasta/.tag_spygen.fasta}"
ecotag -d "$REF_DATABASE"/"${base_pref}" -R "$spygen_bdr_fasta" $dereplicated_all > $all_sample_sequences_tag_spygen
##The sequences can be sorted by decreasing order of count
all_sample_sequences_sort="${all_sample_sequences_tag-spygen/.fasta/.sort.fasta}"
all_sample_sequences_sort="${all_sample_sequences_tag_spygen/.fasta/.sort.fasta}"
obisort -k count -r $all_sample_sequences_tag > $all_sample_sequences_sort
##generate a table final results
obitab -o $all_sample_sequences_sort > final/all-spygen.csv
obitab -o $all_sample_sequences_sort > final/all_spygen.csv
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