From d784b6b6e94aea719b202f00e1a0ca69e01d0d92 Mon Sep 17 00:00:00 2001
From: julien lagarde <julienlag@gmail.com>
Date: Mon, 13 Sep 2021 11:46:43 +0200
Subject: [PATCH] add setup_LRGASP.sh

---
 setup_LRGASP.sh | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 setup_LRGASP.sh

diff --git a/setup_LRGASP.sh b/setup_LRGASP.sh
new file mode 100644
index 0000000..316d54d
--- /dev/null
+++ b/setup_LRGASP.sh
@@ -0,0 +1,20 @@
+# cd to your working directory, then:
+
+mkdir fastqs
+mkdir genomes
+cd genomes
+#download genomes
+cd genomes
+synapse get syn25683364  
+synapse get syn25683365
+zcat lrgasp_grch38_sirvs.fasta.gz >hg38.fa
+zcat lrgasp_grcm39_sirvs.fasta.gz > mm10.fa
+cd ..
+
+cd fastqs 
+# name fastqs according to sample_name values in sample_annotations_LRGASP.tsv
+
+cd ..
+
+# follow further instructions in https://github.com/julienlag/LyRic to install and execute LyRic
+