add setup_LRGASP.sh

guigolab · Sep 13, 2021 · d784b6b · d784b6b
1 parent 38bf092
commit d784b6b
Showing 1 changed file with 20 additions and 0 deletions.
diff --git a/setup_LRGASP.sh 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
+