diff --git a/workflow/rules/assigned_counts.smk b/workflow/rules/assigned_counts.smk
index 61277fa..6be84a7 100644
--- a/workflow/rules/assigned_counts.smk
+++ b/workflow/rules/assigned_counts.smk
@@ -62,7 +62,7 @@ rule assigned_counts_assignBarcodes:
     conda:
         "../envs/python3.yaml"
     input:
-        counts=lambda wc: getFinalCounts(wc.project, wc.config, wc.type, "counts"),
+        counts=lambda wc: getFinalCounts(wc.project, wc.config, wc.condition, wc.type, "counts"),
         association="results/experiments/{project}/assignment/{assignment}.tsv.gz",
         script=getScript("count/merge_BC_and_assignment.py"),
     output:
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index c4efcce..d62638b 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -276,15 +276,16 @@ def getOutputConditionReplicateType_helper(files, project, skip={}):
             return []
     conditions = getConditions(project)
     for condition in conditions:
-        replicates = getReplicatesOfCondition(project, condition)
         for file in files:
-            output += expand(
-                file,
-                project=project,
-                condition=condition,
-                replicate=replicates,
-                type=["RNA", "DNA"],
-            )
+            for type in ["DNA", "RNA"]:
+                replicates = getReplicatesOfConditionType(project, condition, type)
+                output += expand(
+                    file,
+                    project=project,
+                    condition=condition,
+                    replicate=replicates,
+                    type=type,
+                )
     return output
 
 
@@ -687,25 +688,46 @@ def counts_getSamplingConfig(project, conf, dna_or_rna, command):
 
     return ""
 
+def getReplicatesOfConditionType(project, condition, rna_or_dna):
+    exp = getExperiments(project)
+
+    replicates = getReplicatesOfCondition(project, condition)
+
+    if f"{rna_or_dna}_BC_F" in exp.columns:
+
+        exp_filter = exp[exp.Condition == condition]
+
+        if len(replicates) > 1 and exp_filter[f"{rna_or_dna}_BC_F"].nunique() == 1:
+            return [replicates[0]]
+
+    return replicates
 
-def getFinalCounts(project, conf, rna_or_dna, raw_or_assigned):
+
+def getFinalCounts(project, conf, condition, rna_or_dna, raw_or_assigned):
     output = ""
+
+    replicates = getReplicatesOfConditionType(project, condition, rna_or_dna)
+    if len(replicates) > 1:
+        replicate = "{replicate}"
+    else:
+        replicate = replicates[0]
+    
     if raw_or_assigned == "counts":
         if useSampling(project, conf, rna_or_dna):
             output = (
-                "results/experiments/{project}/%s/{condition}_{replicate}_%s_final_counts.sampling.{config}.tsv.gz"
-                % (raw_or_assigned, rna_or_dna)
+                "results/experiments/{project}/%s/{condition}_%s_%s_final_counts.sampling.{config}.tsv.gz"
+                % (raw_or_assigned, replicate, rna_or_dna)
             )
 
         else:
             output = (
-                "results/experiments/{project}/%s/{condition}_{replicate}_%s_final_counts.tsv.gz"
-                % (raw_or_assigned, rna_or_dna)
+                "results/experiments/{project}/%s/{condition}_%s_%s_final_counts.tsv.gz"
+                % (raw_or_assigned, replicate, rna_or_dna)
             )
     else:
         output = (
-            "results/experiments/{project}/%s/{condition}_{replicate}_%s_final_counts.config.{config}.tsv.gz"
-            % (raw_or_assigned, rna_or_dna)
+            "results/experiments/{project}/%s/{condition}_%s_%s_final_counts.config.{config}.tsv.gz"
+            % (raw_or_assigned, replicate, rna_or_dna)
         )
     return output
 
@@ -733,20 +755,6 @@ def assignedCounts_getAssignmentSamplingConfig(project, assignment, command):
 # statistic.smk specific functions
 
 
-# get all counts of experiment (rule statistic_counts)
-def getCountStats(project, countType):
-    exp = getExperiments(project)
-    output = []
-    for index, row in exp.iterrows():
-        output += expand(
-            "results/experiments/{{project}}/statistic/counts/{condition}_{replicate}_{type}_{{countType}}_counts.tsv.gz",
-            condition=row["Condition"],
-            replicate=row["Replicate"],
-            type=["DNA", "RNA"],
-        )
-    return output
-
-
 # get all barcodes of experiment (rule statistic_BC_in_RNA_DNA)
 def getBCinRNADNAStats(wc):
     exp = getExperiments(wc.project)
diff --git a/workflow/rules/counts.smk b/workflow/rules/counts.smk
index bc82472..f85b186 100644
--- a/workflow/rules/counts.smk
+++ b/workflow/rules/counts.smk
@@ -110,8 +110,8 @@ rule counts_dna_rna_merge_counts:
     conda:
         "../envs/default.yaml"
     input:
-        dna=lambda wc: getFinalCounts(wc.project, wc.config, "DNA", wc.raw_or_assigned),
-        rna=lambda wc: getFinalCounts(wc.project, wc.config, "RNA", wc.raw_or_assigned),
+        dna=lambda wc: getFinalCounts(wc.project, wc.config, wc.condition, "DNA", wc.raw_or_assigned),
+        rna=lambda wc: getFinalCounts(wc.project, wc.config, wc.condition, "RNA", wc.raw_or_assigned),
     output:
         "results/experiments/{project}/{raw_or_assigned}/{condition}_{replicate}.merged.config.{config}.tsv.gz",
     params:
diff --git a/workflow/rules/statistic/bc_overlap.smk b/workflow/rules/statistic/bc_overlap.smk
index 7ac65bd..d76e59a 100644
--- a/workflow/rules/statistic/bc_overlap.smk
+++ b/workflow/rules/statistic/bc_overlap.smk
@@ -8,7 +8,7 @@ rule statistic_bc_overlap_run:
         "../../envs/r.yaml"
     input:
         files=lambda wc: expand(
-            getFinalCounts(wc.project, wc.config, wc.type, wc.raw_or_assigned),
+            getFinalCounts(wc.project, wc.config, wc.condition, wc.type, wc.raw_or_assigned),
             project=wc.project,
             condition=wc.condition,
             config=wc.config,
@@ -22,7 +22,7 @@ rule statistic_bc_overlap_run:
     params:
         input=lambda wc: ",".join(
             expand(
-                getFinalCounts(wc.project, wc.config, wc.type, wc.raw_or_assigned),
+                getFinalCounts(wc.project, wc.config, wc.condition, wc.type, wc.raw_or_assigned),
                 project=wc.project,
                 condition=wc.condition,
                 config=wc.config,
@@ -31,7 +31,7 @@ rule statistic_bc_overlap_run:
         ),
         cond="{condition}_{type}",
         replicates=lambda wc: ",".join(
-            getReplicatesOfCondition(wc.project, wc.condition)
+            getReplicatesOfConditionType(wc.project, wc.condition, wc.type)
         ),
     log:
         temp(
diff --git a/workflow/rules/statistic/counts.smk b/workflow/rules/statistic/counts.smk
index d03b654..60c1fd9 100644
--- a/workflow/rules/statistic/counts.smk
+++ b/workflow/rules/statistic/counts.smk
@@ -1,3 +1,6 @@
+include: "counts_common.smk"
+
+
 #################################
 ## count 10 most frequent UMIs ##
 #################################
@@ -148,15 +151,11 @@ rule statistic_counts_BC_in_RNA_DNA:
     conda:
         "../../envs/default.yaml"
     input:
-        dna=lambda wc: (
-            "results/experiments/{project}/counts/{condition}_{replicate}_DNA_{countType}_counts.tsv.gz"
-            if wc.countType != "raw"
-            else getRawCounts(wc.project, "DNA")
+        dna=lambda wc: statistic_counts_BC_in_RNA_DNA_helper(
+            project, wc.condition, "DNA", wc.countType
         ),
-        rna=lambda wc: (
-            "results/experiments/{project}/counts/{condition}_{replicate}_RNA_{countType}_counts.tsv.gz"
-            if wc.countType != "raw"
-            else getRawCounts(wc.project, "RNA")
+        rna=lambda wc: statistic_counts_BC_in_RNA_DNA_helper(
+            project, wc.condition, "RNA", wc.countType
         ),
     output:
         temp(
diff --git a/workflow/rules/statistic/counts_common.smk b/workflow/rules/statistic/counts_common.smk
new file mode 100644
index 0000000..fba9534
--- /dev/null
+++ b/workflow/rules/statistic/counts_common.smk
@@ -0,0 +1,37 @@
+def statistic_counts_BC_in_RNA_DNA_helper(project, condition, dna_or_rna, countType):
+
+    replicates = getReplicatesOfConditionType(project, condition, dna_or_rna)
+
+    if countType == "raw":
+        output = getRawCounts(project, dna_or_rna)
+    else:
+        output = (
+            "results/experiments/{project}/counts/{condition}_{replicate}_%s_{countType}_counts.tsv.gz"
+            % dna_or_rna
+        )
+
+    if len(replicates) == 1:
+        output = output.replace("{replicate}", replicates[0])
+
+    return output
+
+
+# get all counts of experiment (rule statistic_counts)
+def getCountStats(project, countType):
+    exp = getExperiments(project)
+    output = []
+    for index, row in exp.iterrows():
+        condition=row["Condition"]
+        for dna_or_rna in ["DNA", "RNA"]:
+            replicates = getReplicatesOfConditionType(project, condition, dna_or_rna)
+            if len(replicates) == 1:
+                replicate = replicates[0]
+            else:
+                replicate = row["Replicate"]
+            output += expand(
+                "results/experiments/{{project}}/statistic/counts/{condition}_{replicate}_{type}_{{countType}}_counts.tsv.gz",
+                condition=condition,
+                replicate=replicate,
+                type=dna_or_rna,
+            )
+    return output
diff --git a/workflow/scripts/count/BCCounts_betweenReplicates.R b/workflow/scripts/count/BCCounts_betweenReplicates.R
index a2f59a9..1089d60 100644
--- a/workflow/scripts/count/BCCounts_betweenReplicates.R
+++ b/workflow/scripts/count/BCCounts_betweenReplicates.R
@@ -1,118 +1,166 @@
-
-
+# This script calculates the overlap statistics between replicates of barcode counts.
+# It uses the optparse library to handle command-line arguments and the tidyverse library for data manipulation.
+#
+# Command-line arguments:
+# -c, --condition: Condition name (character)
+# -f, --files: Comma-separated input files of assigned counts (character)
+# -r, --replicates: Comma-separated names of the replicates (same order as files) (character)
+# -o, --outfile: Output file of the correlation table (character)
+#
+# The script performs the following steps:
+# 1. Parse command-line arguments and check for required arguments.
+# 2. Read the input files and replicates.
+# 3. If the number of files does not match the number of replicates, stop with an error.
+# 4. Create a data frame with the files, replicates, and condition.
+# 5. Define functions to:
+#    - Calculate overlap statistics between two data sets (get_overlap_stats).
+#    - Read data from a file (read_data).
+#    - Write the output to a file (write_output).
+# 6. If there is more than one replicate, perform pairwise comparisons:
+#    - Generate all pairwise combinations of replicates.
+#    - For each pair, read the data, calculate overlap statistics, and store the results.
+#    - Calculate the mean Lincoln-Peterson estimator and write the results to the output file.
+# 7. If there is only one replicate, create a single row with NA values for overlap statistics and write it to the output file.
 library(optparse)
 library(tidyverse)
-#library(viridis)
+# library(viridis)
 
 
 option_list <- list(
-    make_option(c("-c", "--condition"), type="character",
-        help="Condition name"),
-    make_option(c("-f", "--files"), type="character",
-        help="Comma separated input files of assigned counts"),
-    make_option(c("-r", "--replicates"), type="character",
-        help="Comma separated name of the replicates (same order than files)"),
-    make_option(c("-o", "--outfile"), type="character",
-        help="Output file of the correlation table.")
+  make_option(c("-c", "--condition"),
+    type = "character",
+    help = "Condition name",
+    metavar = "character"
+  ),
+  make_option(c("-f", "--files"),
+    type = "character",
+    help = "Comma separated input files of assigned counts",
+    metavar = "character"
+  ),
+  make_option(c("-r", "--replicates"),
+    type = "character",
+    help = "Comma separated name of the replicates (same order than files)",
+    metavar = "character"
+  ),
+  make_option(c("-o", "--outfile"),
+    type = "character",
+    help = "Output file of the correlation table.",
+    metavar = "character"
+  )
 )
 
-parser <- OptionParser(option_list=option_list)
-arguments <- parse_args(parser, positional_arguments=TRUE)
+parser <- OptionParser(option_list = option_list)
+arguments <- parse_args(parser, positional_arguments = TRUE)
 opt <- arguments$options
 
-if (!"condition" %in% names(opt)) {
-  stop("--condition parameter must be provided. See script usage (--help)")
-}
-if (!"files" %in% names(opt)) {
-  stop("--files parameter must be provided. See script usage (--help)")
-}
-if (!"replicates" %in% names(opt)) {
-  stop("--replicates parameter must be provided. See script usage (--help)")
-}
-if (!"outfile" %in% names(opt)) {
-  stop("--outfile parameter must be provided. See script usage (--help)")
+required_args <- c("condition", "files", "replicates", "outfile")
+missing_args <- setdiff(required_args, names(opt))
+
+if (length(missing_args) > 0) {
+  stop(paste("Missing required arguments:", paste(missing_args, collapse = ", "), ". See script usage (--help)"))
 }
 
 # condition
-cond=opt$condition
+cond <- opt$condition
 # outfile
-outfile=opt$outfile
+outfile <- opt$outfile
 # replicates and count files
-files <- strsplit(opt$files,",")[[1]]
-replicates=strsplit(opt$replicates,",")[[1]]
+files <- strsplit(opt$files, ",")[[1]]
+replicates <- strsplit(opt$replicates, ",")[[1]]
 if (length(files) != length(replicates)) {
-    stop("Number of input files must be euqal to number of replicates")
+  stop("Number of input files must be euqal to number of replicates")
 }
 
-num_replicates=length(replicates)
+num_replicates <- length(replicates)
 
-data <- data.frame(File=files,Replicate=replicates)
+data <- data.frame(File = files, Replicate = replicates)
 data$Condition <- cond
 
 
-getOverlapStats <- function(data1,data2,condition,r1,r2){
-  sData1 <- data1 %>% summarize(size=n(), count=sum(Counts))
-  print(sData1)
-  sData2 <- data2 %>% summarize(size=n(), count=sum(Counts))
-  print(sData2)
-  data <- data1 %>% inner_join(data2,by=c('Barcode'))
-  sData <- data %>% summarize(size=n(), count1=sum(Counts.x),count2=sum(Counts.y))
-  print(sData)
-  print(sData$count1)
-  print(sData$count1[1])
+get_overlap_stats <- function(data1, data2, condition, r1, r2) {
+  s_data1 <- data1 %>% summarize(size = n(), count = sum(Counts))
+  print(s_data1)
+  s_data2 <- data2 %>% summarize(size = n(), count = sum(Counts))
+  print(s_data2)
+  data <- data1 %>% inner_join(data2, by = c("Barcode"))
+  s_data <- data %>% summarize(size = n(), count1 = sum(Counts.x), count2 = sum(Counts.y))
+  print(s_data)
+  print(s_data$count1)
+  print(s_data$count1[1])
   outs <- data.frame(
-                Condition = condition,
-                ReplicateA = r1,
-                ReplicateB = r2,
-                BCs_ReplicateA = sData1$size,
-                BCs_ReplicateB = sData2$size,
-                BCs_Overlap = sData$size,
-                Counts_ReplicateA = sData1$count,
-                Counts_ReplicateB = sData2$count,
-                Counts_OverlapA = sData$count1,
-                Counts_OverlapB = sData$count2,
-                Overlap_BC_ReplicateA = (sData$size / sData1$size),
-                Overlap_BC_ReplicateB = (sData$size / sData2$size),
-                Overlap_Counts_ReplicateA = (sData$count1 / sData1$count),
-                Overlap_Counts_ReplicateB = (sData$count2 / sData2$count),
-                Lincoln_Peterson_estimator = round(sData1$size * (sData2$size/sData$size)),
-                stringsAsFactors=FALSE)
+    Condition = condition,
+    ReplicateA = r1,
+    ReplicateB = r2,
+    BCs_ReplicateA = s_data1$size,
+    BCs_ReplicateB = s_data2$size,
+    BCs_Overlap = s_data$size,
+    Counts_ReplicateA = s_data1$count,
+    Counts_ReplicateB = s_data2$count,
+    Counts_OverlapA = s_data$count1,
+    Counts_OverlapB = s_data$count2,
+    Overlap_BC_ReplicateA = (s_data$size / s_data1$size),
+    Overlap_BC_ReplicateB = (s_data$size / s_data2$size),
+    Overlap_Counts_ReplicateA = (s_data$count1 / s_data1$count),
+    Overlap_Counts_ReplicateB = (s_data$count2 / s_data2$count),
+    Lincoln_Peterson_estimator = round(s_data1$size * (s_data2$size / s_data$size)),
+    stringsAsFactors = FALSE
+  )
   return(outs)
-
 }
 
-readData <- function(file) {
-  data <- read.table(file,sep="\t",as.is=T,header=F,stringsAsFactors = F)
-  colnames(data) <- c("Barcode","Counts")
+read_data <- function(file) {
+  data <- read.table(file, sep = "\t", as.is = T, header = F, stringsAsFactors = F)
+  colnames(data) <- c("Barcode", "Counts")
   return(data)
 }
 
-writeOutput <- function(correlations, name){
-    write.table(correlations,file=name,quote=FALSE,sep='\t',row.names=FALSE,col.names=TRUE )
+write_output <- function(correlations, name) {
+  write.table(correlations, file = name, quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE)
 }
 
 # pairwise comparison only if more than one replicate
-if(data %>% nrow >1){
-
+if (data %>% nrow() > 1) {
   # make pairwise combinations
-  selected <- combn(data$Replicate,2)
-  print('sel')
+  selected <- combn(data$Replicate, 2)
+  print("sel")
   print(selected)
 
-  overlapStats = data.frame()
-  print('reps')
-  for(i in seq(1,dim(selected)[2])){
-    print(selected[,i])
-    r1=selected[1,i]
-    r2=selected[2,i]
-    data1 <- readData(as.character((data %>% filter(Replicate == r1))$File))
+  overlap_stats <- data.frame()
+  print("reps")
+  for (i in seq(1, dim(selected)[2])) {
+    print(selected[, i])
+    r1 <- selected[1, i]
+    r2 <- selected[2, i]
+    data1 <- read_data(as.character((data %>% filter(Replicate == r1))$File))
     print("Read data 1")
-    data2 <- readData(as.character((data %>% filter(Replicate == r2))$File))
+    data2 <- read_data(as.character((data %>% filter(Replicate == r2))$File))
     print("Read data 2")
-    
-    overlapStats_new <- getOverlapStats(data1, data2, cond,r1,r2)
-    overlapStats <- overlapStats %>% bind_rows(overlapStats_new)
+
+    overlap_stats_new <- get_overlap_stats(data1, data2, cond, r1, r2)
+    overlap_stats <- overlap_stats %>% bind_rows(overlap_stats_new)
   }
-  overlapStats$Mean_Lincoln_Peterson_estimator <- mean(overlapStats$Lincoln_Peterson_estimator)
-  writeOutput(overlapStats, outfile)
+  overlap_stats$Mean_Lincoln_Peterson_estimator <- mean(overlap_stats$Lincoln_Peterson_estimator)
+  write_output(overlap_stats, outfile)
+} else {
+  # If only one replicate, create a single row with NA values for overlap statistics
+  single_replicate_stats <- data.frame(
+    Condition = cond,
+    ReplicateA = replicates[1],
+    ReplicateB = NA,
+    BCs_ReplicateA = NA,
+    BCs_ReplicateB = NA,
+    BCs_Overlap = NA,
+    Counts_ReplicateA = NA,
+    Counts_ReplicateB = NA,
+    Counts_OverlapA = NA,
+    Counts_OverlapB = NA,
+    Overlap_BC_ReplicateA = NA,
+    Overlap_BC_ReplicateB = NA,
+    Overlap_Counts_ReplicateA = NA,
+    Overlap_Counts_ReplicateB = NA,
+    Lincoln_Peterson_estimator = NA,
+    Mean_Lincoln_Peterson_estimator = NA,
+    stringsAsFactors = FALSE
+  )
+  write_output(single_replicate_stats, outfile)
 }