From b8336818637dd8b6cc478e09429ace4ce62e6cf4 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 20 May 2018 19:47:03 -0500
Subject: [PATCH] Add D27 bash script

---
 bash.scripts/sc_FullAnalysis-D27PrF.sh | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100755 bash.scripts/sc_FullAnalysis-D27PrF.sh

diff --git a/bash.scripts/sc_FullAnalysis-D27PrF.sh b/bash.scripts/sc_FullAnalysis-D27PrF.sh
new file mode 100755
index 0000000..3471438
--- /dev/null
+++ b/bash.scripts/sc_FullAnalysis-D27PrF.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+#SBATCH --job-name R_FullAnalysis
+#SBATCH -p 256GB,256GBv1,384GB
+#SBATCH -N 1
+#SBATCH -t 7-0:0:0
+#SBATCH -o job_%j.out
+#SBATCH -e job_%j.out
+#SBATCH --mail-type ALL
+#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
+
+module load R/3.4.1-gccmkl
+
+Rscript ../r.scripts/sc_Demultiplex.R --p="D27PrF" --d=3
+Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R --p="D27PrF"
+Rscript ../r.scripts/sc_QC.R --p="D27PrF"
+Rscript ../r.scripts/sc_Cluster.R --p="D27PrF" --pc=0
+Rscript ../r.scripts/sc_PC.Score.Stress.R --p="D27PrF" --r=0.5 --pc=0 --u=TRUE
+Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="D27PrF" --gs="sc" --r=0.1 --s=NA
+Rscript ../r.scripts/sc_LineageSubClust.R --p="D27PrF" --pc=0
+Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="D27PrF" --r=0.2 --s=NA --sc=TRUE
+Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="D27PrF" --r=0.2 --s=NA --sc=TRUE
+Rscript ../r.scripts/sc_MergeSubClust.R --p="D27PrF" --e="sc" --s="sc"
+Rscript ../r.scripts/sc_PC.Score.NE.R --p="D27PrF" --u=TRUE
+Rscript ../r.scripts/sc_DEG.R --p="D27PrF"
+Rscript ../r.scripts/sc_Tables.R --p="D27PrF"
-- 
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