diff --git a/.DS_Store b/.DS_Store
index e34fb84..61aaf17 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/sceptre_paper/.DS_Store b/sceptre_paper/.DS_Store
index fdaaac1..3975cfa 100644
Binary files a/sceptre_paper/.DS_Store and b/sceptre_paper/.DS_Store differ
diff --git a/sceptre_paper/analysis_drivers/.DS_Store b/sceptre_paper/analysis_drivers/.DS_Store
index 90ead10..f545405 100644
Binary files a/sceptre_paper/analysis_drivers/.DS_Store and b/sceptre_paper/analysis_drivers/.DS_Store differ
diff --git a/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R b/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R
index 2e8bb08..5304f86 100644
--- a/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R
+++ b/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R
@@ -4,7 +4,9 @@ offsite_dir <- .get_config_path("LOCAL_SCEPTRE_DATA_DIR")
 library(monocle)
 source(paste0(code_dir, "/sceptre_paper/analysis_drivers/analysis_drivers_xie/paths_to_dirs.R"))
 source(paste0(code_dir, "/sceptre_paper/analysis_drivers/analysis_drivers_xie/gasp_custom_functs.R"))
-cds <- readRDS(paste0(processed_dir, "/monocole_obj.rds"))
+analysis_ready_dir <- paste0(offsite_dir, "data/xie/analysis_ready")
+
+cds <- readRDS(paste0(analysis_ready_dir, "/monocole_obj.rds"))
 pairs <- fst::read_fst(paste0(processed_dir, "/gRNA_gene_pairs.fst"))
 pairs <- pairs[1:100,]
 
@@ -32,4 +34,4 @@ res <- purrr::map_dfr(.x = seq(1, nrow(pairs)), .f = function(i) {
   return(out)
 })
 
-saveRDS(res, paste0(results_dir_negative_binomial, "/monocle_nb_results.rds"))
\ No newline at end of file
+saveRDS(res, paste0(results_dir_negative_binomial, "/monocle_nb_results.rds"))
diff --git a/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R b/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R
index be24898..a5ada71 100644
--- a/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R
+++ b/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R
@@ -1,11 +1,11 @@
 # offsite_dir <- .get_config_path("LOCAL_SCEPTRE_DATA_DIR")
-small_example <- FALSE
+small_example <- TRUE
 library(sceptre)
 
 processed_dir <- paste0(offsite_dir, "/data/xie/processed")
 analysis_ready_dir <- paste0(offsite_dir, "/data/xie/analysis_ready")
 results_dir_negbin <- paste0(offsite_dir, "/results/xie/negative_binomial")
-bulk_regions <- readRDS(paste0(processed_dir, "/bulk_region_names.rds"))
+bulk_regions <- readRDS(paste0(plrocessed_dir, "/bulk_region_names.rds"))
 gRNA_gene_pairs <- fst::read.fst(paste0(processed_dir, "/gRNA_gene_pairs.fst"))
 covariate_matrix <- fst::read.fst(paste0(analysis_ready_dir, "/covariate_model_matrix.fst"))
 cell_gene_expression_matrix_info <- readRDS(paste0(analysis_ready_dir, "/exp_mat_sub_metadata.rds")) 
diff --git a/sceptre_paper/utilities/run_xie_analysis.bash b/sceptre_paper/utilities/run_xie_analysis.bash
index 9743b3a..7a73192 100644
--- a/sceptre_paper/utilities/run_xie_analysis.bash
+++ b/sceptre_paper/utilities/run_xie_analysis.bash
@@ -7,6 +7,7 @@ source ~/.research_config
 # Set the number of processors.
 n_processors=50
 machine=$MACHINE_NAME
+precomputation_complete=FALSE
 
 echo Running on machine $machine with $n_processors processors.
 
@@ -22,23 +23,22 @@ bash build_and_install_package.bash sceptre $machine
 bash build_and_install_package.bash katsevich2020 $machine
 
 echo Initialize the offsite directory structure.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"check_directory_structure_1.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"check_directory_structure_1.R
 
 echo Download the data.
 # Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"download_data_2.R
 
 echo Pre-process the data.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"pre_process_data_3.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"pre_process_data_3.R
 
 echo Construct model covariate matrix and perform quality control.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"quality_control_4.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"quality_control_4.R
 
 echo Determine the gene-gRNA pairs to analyze.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"select_gRNA_gene_pair_5.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"select_gRNA_gene_pair_5.R
 
 echo Create monocole object for monocole NB analysis.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"create_monocle_object_5.1.R
-
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"create_monocle_object_5.1.R
 
 # Locate the parameter file
 parameter_file=$code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"sceptre_function_args.R