From b6551f07bc039d8b301772b6730fd5600aa2a0c2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 9 Oct 2018 15:51:09 +0200
Subject: [PATCH] 1_JU28_59vs17_SNP_calling.sh: blast of 5S on the assembly

---
 src/1_JU28_59vs17_SNP_calling.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh
index 42f5adb..61e11d4 100644
--- a/src/1_JU28_59vs17_SNP_calling.sh
+++ b/src/1_JU28_59vs17_SNP_calling.sh
@@ -27,3 +27,8 @@ src/intersect_SNP.R \
   data/list_of_enzymes.csv
 ~/scripts/sms.sh "SNP analysis done"
 
+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
+
-- 
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