From 5d990d3204c1391183d7e326e2d7e29ba78c7447 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 9 Oct 2018 17:20:57 +0200
Subject: [PATCH] 1_JU28_59vs17_SNP_calling.sh: test of blast

---
 src/1_JU28_59vs17_SNP_calling.sh | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh
index 61e11d4..44d2edc 100644
--- a/src/1_JU28_59vs17_SNP_calling.sh
+++ b/src/1_JU28_59vs17_SNP_calling.sh
@@ -29,6 +29,13 @@ src/intersect_SNP.R \
 
 mkdir -p results/blastall/
 makeblastdb -in data/fasta/DBG2OLC_output2.fasta -parse_seqids -dbtype nucl
-blastn -query data/RNA5S_belari.fasta -db data/fasta/DBG2OLC_output2.fasta -out results/blastall/RNA5S.out
-less results/blastall/RNA5S.out
+blastn -query data/RNA5S_belari.fasta -db data/fasta/DBG2OLC_output2.fasta -out results/blastall/RNA5S_2.out
+less results/blastall/RNA5S_2.out
 
+makeblastdb -in data/fasta/DBG2OLC_output1.fasta -parse_seqids -dbtype nucl
+blastn -query data/RNA5S_belari.fasta -db data/fasta/DBG2OLC_output1.fasta -out results/blastall/RNA5S_1.out
+less results/blastall/RNA5S_1.out
+
+makeblastdb -in data/fasta/nanoport_denovo.fasta -parse_seqids -dbtype nucl
+blastn -query data/RNA5S_belari.fasta -db data/fasta/nanoport_denovo.fasta -out results/blastall/RNA5S_nanoport.out
+less results/blastall/RNA5S_nanoport.out
-- 
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