From 721e404673741e3831d1065649763b044bf69d88 Mon Sep 17 00:00:00 2001 From: nicolas-zimmermann Date: Thu, 24 Oct 2019 12:15:12 +0200 Subject: [PATCH] added annotation part --- 16S_workflow.sh | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/16S_workflow.sh b/16S_workflow.sh index 81bee32..746699b 100755 --- a/16S_workflow.sh +++ b/16S_workflow.sh @@ -48,7 +48,10 @@ soft/vsearch --uchime_denovo fasta/prefix.fasta --nonchimeras fasta/prefix_nochi # CLUSTERING otu=">OTU_" -vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/centroids.fasta --relabel $otu +vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/otu.fasta --relabel $otu # ABONDANCE -vsearch --usearch_global fasta/amplicon.fasta --db otu/clusters.fasta --id 0.97 --otutabout otu/abondance_table.txt +vsearch --usearch_global fasta/amplicon.fasta --db otu/otu.fasta --id 0.97 --otutabout otu/abondance_table.txt + +# ANNOTATION +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