V1.3.1 released

wbaopaul · May 21, 2021 · 0a77b85 · 0a77b85
1 parent f0abcef
commit 0a77b85
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Showing 8 changed files with 37 additions and 40 deletions.
diff --git a/scripts/addQC2seurat.sh b/scripts/addQC2seurat.sh
diff --git 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
@@ -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
@@ -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 $3
+
+
diff --git a/scripts/process_no_dex.sh b/scripts/process_no_dex.sh
@@ -75,13 +75,17 @@ echo "call cell ..."
 mat_file=${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
@@ -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
@@ -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
@@ -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)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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

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