From 741269e63078014763b4fac7cf34f1504115092a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 11 Oct 2018 11:16:46 +0200
Subject: [PATCH] 1_JU28_59vs17_SNP_calling.sh: add PSMN cmd
---
src/1_JU28_59vs17_SNP_calling.sh | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh
index 44d2edce..93de93b8 100644
--- a/src/1_JU28_59vs17_SNP_calling.sh
+++ b/src/1_JU28_59vs17_SNP_calling.sh
@@ -27,6 +27,14 @@ src/intersect_SNP.R \
data/list_of_enzymes.csv
~/scripts/sms.sh "SNP analysis done"
+
+# on the PSMN
+find ~/data/ -name "MR_350_clean*"
+find ~/data/ -name "MR_550_clean*"
+find ~/data/ -name "10944_JU2859_bis_lib169352_5217_1*"
+
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile sge --fasta "data/fasta/final_assembly.fasta" --fastq "/Xnfs/lbmcdb/Delattre_team/Request/Clean_data_for_assembly/*_{1,2}.fastq.gz" -resume -w /scratch/lmodolo/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\", \"MR_350_clean\"]"
+
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_2.out
--
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