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16S_workflow
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ajout commandes

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nicolas-zimmermann 2019-10-23 17:44:58 +02:00
parent a84bce7c31
commit 21880df223
1 changed files with 8 additions and 4 deletions
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16S_workflow.sh
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@ -37,9 +37,13 @@ sed -i 's/ //g' fasta/amplicon.fasta
# CREATE OTU
# DEDUPLICATION
mkdir otu
soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu
soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu
soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu.fasta
soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu.fasta
# REMOVING SINGLETON
soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu --minuniquesize 10
soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu --minuniquesize 10
soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu.fasta --minuniquesize 10
soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu.fasta --minuniquesize 10
# REMOVING CHIMERAS
soft/vsearch --uchime_denovo otu/prefix_min10_otu.fasta --nonchimeras otu/prefix_min10_nochim_otu.fasta
soft/vsearch --uchime_denovo otu/fulllength_min10_otu.fasta --nonchimeras otu/fulllength_min10_nochim_otu.fasta