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|
37
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# CREATE OTU
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37
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# CREATE OTU
|
38
|
# DEDUPLICATION
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38
|
# DEDUPLICATION
|
39
|
mkdir otu
|
39
|
mkdir otu
|
40
|
-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu
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|
|
41
|
-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu
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|
|
|
|
40
|
+soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu.fasta
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|
|
41
|
+soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu.fasta
|
42
|
|
42
|
|
43
|
# REMOVING SINGLETON
|
43
|
# REMOVING SINGLETON
|
44
|
-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu --minuniquesize 10
|
|
|
45
|
-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu --minuniquesize 10
|
|
|
|
|
44
|
+soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu.fasta --minuniquesize 10
|
|
|
45
|
+soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu.fasta --minuniquesize 10
|
|
|
46
|
+
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|
|
47
|
+# REMOVING CHIMERAS
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|
|
48
|
+soft/vsearch --uchime_denovo otu/prefix_min10_otu.fasta --nonchimeras otu/prefix_min10_nochim_otu.fasta
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|
|
49
|
+soft/vsearch --uchime_denovo otu/fulllength_min10_otu.fasta --nonchimeras otu/fulllength_min10_nochim_otu.fasta
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