From 21880df2239a140c9f6d87898fd64225249a608b Mon Sep 17 00:00:00 2001 From: nicolas-zimmermann Date: Wed, 23 Oct 2019 17:44:58 +0200 Subject: [PATCH] ajout commandes --- 16S_workflow.sh | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/16S_workflow.sh b/16S_workflow.sh index 991a922..6ea9f35 100755 --- a/16S_workflow.sh +++ b/16S_workflow.sh @@ -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