diff --git a/scripts/addQC2seurat.sh b/scripts/addQC2seurat.sh
deleted file mode 100644
index 89c4ca6..0000000
--- a/scripts/addQC2seurat.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-
-## reconstruct peak-cell matrix given a union peak file, a fragment.txt file and
-## a barcodes.txt file, separated by comma
-## the output peak-by-cell matrix will be saved under reConstruct_Matrix/, which
-## was under the same directory as barcodes.txt file
-
-set -e
-
-inputs=$1 
-
-inputs=(${inputs//,/ })
-seurat_file=${inputs[0]}
-qc_file=${inputs[1]}
-
-# reading configure file
-curr_dir=`dirname $0`
-source ${curr_dir}/read_conf.sh
-read_conf "$2"
-read_conf "$3"
-
-
-${R_PATH}/R --vanilla --args $seurat_file $qc_file < ${curr_dir}/src/addQC2seurat.R 
-
diff --git a/scripts/downstream.sh b/scripts/downstream.sh
index 98c2086..aefe83f 100755
--- a/scripts/downstream.sh
+++ b/scripts/downstream.sh
@@ -13,6 +13,7 @@ read_conf $3
 
 frag_file=${OUTPUT_DIR}/summary/${OUTPUT_PREFIX}.fragments.tsv.gz
 
+
 ## clustering
 ${curr_dir}/clustering.sh $input_mtx $2 $3 
 
diff --git a/scripts/integrate_peak.sh b/scripts/integrate_peak.sh
index 9981cc4..3b7dc39 100755
--- a/scripts/integrate_peak.sh
+++ b/scripts/integrate_peak.sh
@@ -50,7 +50,10 @@ do
     frag0_file=$(find $frag0_dir -name "*fragments*" | grep -v "\.len")
     mat0_dir=${mat0_dir}/${PEAK_CALLER}/${CELL_CALLER}
     #bc0_file=$(find ${mat0_dir} -name "*barcodes.txt")
-    bc0_file=${mat0_dir}/barcodes.txt
+    bc0_file=${mat0_dir}/barcodes_doubletsRemoved.txt
+    if [ ! -e "$bc0_file" ]; then
+         bc0_file=${mat0_dir}/barcodes.txt 
+    fi
     bash ${curr_dir}/reConstMtx.sh ${feature_file},${frag0_file},${bc0_file} $2 $3
     mtx_files=${mtx_files},${mat0_dir}/reConstruct_matrix/matrix.mtx
 done
diff --git a/scripts/process.sh b/scripts/process.sh
index 2336b71..39aa215 100755
--- a/scripts/process.sh
+++ b/scripts/process.sh
@@ -77,12 +77,19 @@ echo "call cell ..."
 mat_file=${OUTPUT_DIR}/raw_matrix/${PEAK_CALLER}/matrix.mtx
 ${curr_dir}/call_cell.sh $mat_file $2 $3 
 
-## 8. mapping qc for cell barcodes
+
+## 8. remove doublets
+filtered_mtx_file=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/matrix.rds
+${curr_dir}/rmDoublets.sh ${filtered_mtx_file},0.03 $2 $3
+
+## 9. mapping qc for cell barcodes
 map_dir=${OUTPUT_DIR}/mapping_result
 input_bam=${map_dir}/${OUTPUT_PREFIX}.positionsort.bam
-input_bc=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/barcodes.txt
+input_bc=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/barcodes_doubletsRemoved.txt
 ${curr_dir}/get_bam4Cells.sh ${input_bam},${input_bc} $2 $3
 
-## report preprocessing QC
+## 10.report preprocessing QC
 echo "generating report ..."
-${curr_dir}/report.sh $OUTPUT_DIR/summary $2 $3
+${curr_dir}/report.sh ${OUTPUT_DIR}/summary $2 $3
+
+
diff --git a/scripts/process_no_dex.sh b/scripts/process_no_dex.sh
index 823e225..a7a0c0a 100755
--- a/scripts/process_no_dex.sh
+++ b/scripts/process_no_dex.sh
@@ -75,13 +75,17 @@ echo "call cell ..."
 mat_file=${OUTPUT_DIR}/raw_matrix/${PEAK_CALLER}/matrix.mtx
 ${curr_dir}/call_cell.sh $mat_file $2 $3
 
-## 8. mapping qc for cell barcodes
+## 8. remove doublets
+filtered_mtx_file=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/matrix.rds
+${curr_dir}/rmDoublets.sh ${filtered_mtx_file},0.03 $2 $3
+
+## 9. mapping qc for cell barcodes
 map_dir=${OUTPUT_DIR}/mapping_result
 input_bam=${map_dir}/${OUTPUT_PREFIX}.positionsort.bam
-input_bc=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/barcodes.txt
+input_bc=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/barcodes_doubletsRemoved.txt
 ${curr_dir}/get_bam4Cells.sh ${input_bam},${input_bc} $2 $3
 
-## report preprocessing QC
+## 10.report preprocessing QC
 echo "generating report ..."
-${curr_dir}/report.sh $OUTPUT_DIR/summary $2 $3
+${curr_dir}/report.sh ${OUTPUT_DIR}/summary $2 $3
 
diff --git a/scripts/process_with_bam.sh b/scripts/process_with_bam.sh
index 1c3788c..2bbc9ab 100755
--- a/scripts/process_with_bam.sh
+++ b/scripts/process_with_bam.sh
@@ -58,14 +58,18 @@ echo "call cell ..."
 mat_file=${OUTPUT_DIR}/raw_matrix/${PEAK_CALLER}/matrix.mtx
 ${curr_dir}/call_cell.sh $mat_file $2 $3
 
-## 6. mapping qc for cell barcodes
+## 6. remove doublets
+filtered_mtx_file=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/matrix.rds
+${curr_dir}/rmDoublets.sh ${filtered_mtx_file},0.03 $2 $3
+
+## 7. mapping qc for cell barcodes
 map_dir=${OUTPUT_DIR}/mapping_result
 input_bam=${map_dir}/${OUTPUT_PREFIX}.positionsort.bam
-input_bc=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/barcodes.txt
+input_bc=${OUTPUT_DIR}/filtered_matrix/${PEAK_CALLER}/${CELL_CALLER}/barcodes_doubletsRemoved.txt
 ${curr_dir}/get_bam4Cells.sh ${input_bam},${input_bc} $2 $3
 
-
-## report preprocessing QC
+## 8.report preprocessing QC
 echo "generating report ..."
-${curr_dir}/report.sh $OUTPUT_DIR/summary $2 $3
+${curr_dir}/report.sh ${OUTPUT_DIR}/summary $2 $3
+
 
diff --git a/scripts/src/rmDoublets.R b/scripts/src/rmDoublets.R
index f164770..818bc32 100644
--- a/scripts/src/rmDoublets.R
+++ b/scripts/src/rmDoublets.R
@@ -9,7 +9,7 @@ source_local('dsAnalysis_utilities.R')
 args = commandArgs(T)
 inputObj_file = args[1] ## a mtx.rds or a seurat.rds file
 drate = as.numeric(args[2])
-if(is.null(drate)) drate = 0.4
+if(is.null(drate)) drate = 0.03
 input.obj = readRDS(inputObj_file)
 if(any(class(input.obj) == 'Seurat')) {
     seurat.obj = input.obj
diff --git a/scripts/src/scATAC-pro_report.Rmd b/scripts/src/scATAC-pro_report.Rmd
index 2986452..cc9398a 100644
--- a/scripts/src/scATAC-pro_report.Rmd
+++ b/scripts/src/scATAC-pro_report.Rmd
@@ -123,7 +123,9 @@ if(file.exists(cell_mapping_qc_file)) cell_mapping_qc = fread(cell_mapping_qc_fi
 
 
 bc_stat_file = paste0(params$output_dir, '/summary/', OUTPUT_PREFIX, '.', PEAK_CALLER, '.qc_per_barcode.txt')
-selected_bcs = paste0(params$output_dir, '/filtered_matrix/', PEAK_CALLER, '/', CELL_CALLER, '/barcodes.txt')
+selected_bcs = paste0(params$output_dir, '/filtered_matrix/', PEAK_CALLER, '/', CELL_CALLER, '/barcodes_doubletsRemoved.txt')
+if(!file.exists(selected_bcs)) selected_bcs = paste0(params$output_dir, '/filtered_matrix/', PEAK_CALLER, '/', CELL_CALLER, '/barcodes.txt')
+
 peak_file = paste0(params$output_dir, '/peaks/', PEAK_CALLER, '/', OUTPUT_PREFIX, '_features_BlacklistRemoved.bed')
 
 bc_stat = fread(bc_stat_file)