diff --git a/bash.scripts/sc_CIAnalysis-Pr.sh b/bash.scripts/sc_CIAnalysis-Pr.sh
deleted file mode 100644
index 79d279acfb6b7f42d334f9fed0c85f1e7d5c9090..0000000000000000000000000000000000000000
--- a/bash.scripts/sc_CIAnalysis-Pr.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name R_CIAnalysis
-#SBATCH -p super
-#SBATCH -N 1
-#SBATCH -t 0-1:0:0
-#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
-Rscript ../r.scritps/sc_D-SampleReorder.R
-Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R
-Rscript ../r.scripts/sc_QC.R
-Rscript ../r.scripts/sc_Cluster.R
-Rscript ../r.scripts/sc_PC.Score.Stress.R --sv=NA
-Rscript ../r.scripts/sc_QuSAGE.Lineage.R --s=NA
-Rscript ../r.scripts/sc_LineageSubClust.R
-Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --s=NA --r=0.2
-Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --s=NA --r=0.2
-Rscript ../r.scripts/sc_MergeSubClust.R --r=0.2
-Rscript ../r.scripts/sc_PC.Score.NE.R --sv=NA
-Rscript ../r.scripts/sc_DEG.R
-Rscript ../r.scripts/sc_Tables.R
diff --git a/bash.scripts/sc_FullAnalysis-D17PrF.sh b/bash.scripts/sc_FullAnalysis-D17PrF.sh
deleted file mode 100755
index 8200e96d107dcbb9605251311ed6dc4bbb8056d7..0000000000000000000000000000000000000000
--- a/bash.scripts/sc_FullAnalysis-D17PrF.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name R_FullAnalysis
-#SBATCH -p 128GB,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="D17PrF" --d=3
-Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R --p="D17PrF"
-Rscript ../r.scripts/sc_QC.R --p="D17PrF"
-Rscript ../r.scripts/sc_Cluster.R --p="D17PrF" --pc=0
-Rscript ../r.scripts/sc_PC.Score.Stress.R --p="D17PrF" --r=0.5 --pc=0
-Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="D17PrF" --r=0.1 --s=NA
-Rscript ../r.scripts/sc_LineageSubClust.R --p="D17PrF" --pc=0
-Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="D17PrF" --r=0.1 --s=NA
-Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="D17PrF" --r=0.1 --s=NA
-Rscript ../r.scripts/sc_MergeSubClust.R --p="D17PrF"
-Rscript ../r.scripts/sc_PC.Score.NE.R --p="D17PrF"
-Rscript ../r.scripts/sc_DEG.R --p="D17PrF"
-Rscript ../r.scripts/sc_Tables.R --p="D17PrF"
diff --git a/bash.scripts/sc_FullAnalysis-D27PrF.sh b/bash.scripts/sc_FullAnalysis-D27PrF.sh
deleted file mode 100755
index 34714385c9d31b40390ed996d6670d58b2f06cd5..0000000000000000000000000000000000000000
--- a/bash.scripts/sc_FullAnalysis-D27PrF.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/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"
diff --git a/bash.scripts/sc_FullAnalysis-DPrF.sh b/bash.scripts/sc_FullAnalysis-DPrF.sh
deleted file mode 100644
index 49f95538d3dd8510c0cf4984d16b4bd84cc77470..0000000000000000000000000000000000000000
--- a/bash.scripts/sc_FullAnalysis-DPrF.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/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="DPrF" --d=3
-#Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R --p="DPrF"
-#Rscript ../r.scripts/sc_QC.R --p="DPrF"
-
-Rscript ../r.scripts/sc_DIY.DPrF.aggr.R
-
-Rscript ../r.scripts/sc_Cluster.R --p="DPrF" --pc=0
-Rscript ../r.scripts/sc_PC.Score.Stress.R --p="DPrF" --r=1 --pc=0 --u=TRUE
-Rscript ../r.scripts/sc_QuSAGE.Lineage.R --p="DPrF" --gs="sc" --r=0.5 --s=NA
-Rscript ../r.scripts/sc_LineageSubClust.R --p="DPrF" --pc=0
-Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R --p="DPrF" --r=1 --s=NA --sc=TRUE
-Rscript ../r.scripts/sc_QuSAGE_StSubClust.R --p="DPrF" --r=1 --s=NA --sc=TRUE
-Rscript ../r.scripts/sc_MergeSubClust.R --p="DPrF" --e="sc" --s="sc"
-Rscript ../r.scripts/sc_PC.Score.NE.R --p="DPrF" --u=TRUE
-#Rscript ../r.scripts/sc_DEG.R --p="DPrF"
-Rscript ../r.scripts/sc_Tables.R --p="DPrF"
diff --git a/bash.scripts/sc_FullAnalysis.sh b/bash.scripts/sc_FullAnalysis.sh
deleted file mode 100755
index 19f4d0379c704a4d1f41b1b88d702e5f0399f5cc..0000000000000000000000000000000000000000
--- a/bash.scripts/sc_FullAnalysis.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name R_FullAnalysis
-#SBATCH -p 128B,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
-Rscript ../r.scripts/sc_Seurat.Score.CellCycle.R
-Rscript ../r.scripts/sc_QC.R
-Rscript ../r.scripts/sc_Cluster.R
-Rscript ../r.scripts/sc_PC.Score.Stress.R
-Rscript ../r.scripts/sc_QuSAGE.Lineage.R
-Rscript ../r.scripts/sc_LineageSubClust.R
-Rscript ../r.scripts/sc_QuSAGE_EpiSubClust.R
-Rscript ../r.scripts/sc_QuSAGE_StSubClust.R
-Rscript ../r.scripts/sc_MergeSubClust.R
-Rscript ../r.scripts/sc_PC.Score.NE.R
-Rscript ../r.scripts/sc_DEG.R
-Rscript ../r.scripts/sc_Tables.R