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16S_workflow
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added annotation part

nicolas-zimmermann 4 years ago
parent
8ff28a2a57
commit
721e404673
1 changed files with 5 additions and 2 deletions
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      16S_workflow.sh

+ 5 - 2
16S_workflow.sh View File 

@@ -48,7 +48,10 @@ soft/vsearch --uchime_denovo fasta/prefix.fasta --nonchimeras fasta/prefix_nochi
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 # CLUSTERING
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 otu=">OTU_"
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-vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/centroids.fasta --relabel $otu
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+vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/otu.fasta --relabel $otu
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 # ABONDANCE
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-vsearch --usearch_global fasta/amplicon.fasta --db otu/clusters.fasta --id 0.97 --otutabout otu/abondance_table.txt
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+vsearch --usearch_global fasta/amplicon.fasta --db otu/otu.fasta --id 0.97 --otutabout otu/abondance_table.txt
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+
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+# ANNOTATION
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+soft/vsearch --usearch_global otu/otu.fasta --db databases/mock_16S_18S.fasta --id 0.97 --top_hits_only --userfields query+target --userout otu/annotation.txt