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16S_workflow
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ajout commandes

nicolas-zimmermann 4 years ago
parent
a84bce7c31
commit
21880df223
1 changed files with 8 additions and 4 deletions
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  1. 8 4
      16S_workflow.sh

+ 8 - 4
16S_workflow.sh View File 

@@ -37,9 +37,13 @@ sed -i 's/ //g' fasta/amplicon.fasta
37 37 
 # CREATE OTU
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 # DEDUPLICATION
39 39 
 mkdir otu
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-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu
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-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu
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+soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu.fasta
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+soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu.fasta
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43 43 
 # REMOVING SINGLETON
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-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu --minuniquesize 10
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-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu --minuniquesize 10
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+soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu.fasta --minuniquesize 10
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+soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu.fasta --minuniquesize 10
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+
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+# REMOVING CHIMERAS
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+soft/vsearch --uchime_denovo otu/prefix_min10_otu.fasta --nonchimeras otu/prefix_min10_nochim_otu.fasta
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+soft/vsearch --uchime_denovo otu/fulllength_min10_otu.fasta --nonchimeras otu/fulllength_min10_nochim_otu.fasta