diff --git a/src/RNAseq.config b/src/RNAseq.config
index a6909dd4b252f54881da1f3eda28a3afc814af3e..7dfd997fab1adb881f634d57e3ca0fca5e55cfac 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -82,8 +82,9 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: dedup_genome {
-          container = "lbmc/umi_tools:1.0.0"
-          executor = "sge"
+          container = "lbmc/hisat2:2.1.0"
+          beforeScript = "source ~/.bashrc"
+ 	  executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1
           memory = "20GB"
@@ -91,7 +92,7 @@ profiles {
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: dedup_postgenome {
-          container = "lbmc/umi_tools:1.0.0"
+          container = "lbmc/hisat2:2.1.0"
           executor = "sge"
           clusterOptions = "-cwd -V"
           cpus = 1
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 7db3b045f6dbd98515c766e4529ec41822e85da4..53edf63dc37a6dafc7445be99a78db25ee79cb6f 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -369,12 +369,17 @@ if (params.do_dedup) {
     when:
     params.do_dedup
 
-      """
-      umi_tools dedup -I ${bam[0]} \
-      -S ${file_id}.dedup.bam \
-      --paired \
-      2> ${file_id}_dedup.log
-      """
+    shell:
+      '''
+      samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | samtools view -bS -o !{file_id}_dedup.bam
+      input=$(samtools view -h !{bam[0]} | wc -l)
+      output=$(samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | wc -l)
+      diff=$(($input - $output))
+      per=$(($diff * 100 / $input))
+      echo "Input : $input reads" > !{file_id}_dedup.log
+      echo "Output : $output reads" >> !{file_id}_dedup.log
+      echo "$per % duplicated reads" >> !{file_id}_dedup.log
+      ''' 
   }
 } else {
   HISAT_ALIGNED_DEDUP.set{DEDUP_GENOME}
@@ -531,12 +536,17 @@ if (params.do_dedup) {
     when:
     params.do_dedup
 
-    """
-    umi_tools dedup -I ${bam[0]} \
-    -S ${file_id}.dedup.bam \
-    --paired \
-    2> ${file_id}_dedup.log
-    """
+    shell:
+      '''
+      samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | samtools view -bS -o !{file_id}_dedup.bam
+      input=$(samtools view -h !{bam[0]} | wc -l)
+      output=$(samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | wc -l)
+      diff=$(($input - $output))
+      per=$(($diff * 100 / $input))
+      echo "Input : $input reads" > !{file_id}_dedup.log
+      echo "Output : $output reads" >> !{file_id}_dedup.log
+      echo "$per % duplicated reads" >> !{file_id}_dedup.log
+      '''
   }
 } else {
 
diff --git a/src/RibosomeProfiling.nf b/src/RibosomeProfiling.nf
index 7f572a23155e9f5e0a7ff39d7803a6f7379edd1e..b65679ec0f30939ce00e31e48761233b2f28ed5c 100644
--- a/src/RibosomeProfiling.nf
+++ b/src/RibosomeProfiling.nf
@@ -353,12 +353,18 @@ if (params.do_dedup) {
 
     when:
     params.do_dedup
-
-      """
-      umi_tools dedup -I ${bam[0]} \
-      -S ${file_id}.dedup.bam \
-      > ${file_id}_dedup.log
-      """
+    
+    shell:
+      '''
+      samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | samtools view -bS -o !{file_id}_dedup.bam
+      input=$(samtools view -h !{bam[0]} | wc -l)
+      output=$(samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | wc -l)
+      diff=$(($input - $output))
+      per=$(($diff * 100 / $input))
+      echo "Input : $input reads" > !{file_id}_dedup.log
+      echo "Output : $output reads" >> !{file_id}_dedup.log
+      echo "$per % duplicated reads" >> !{file_id}_dedup.log
+      '''
   }
 } else {
   HISAT_ALIGNED_DEDUP.set{DEDUP_GENOME}
@@ -513,12 +519,19 @@ if (params.do_dedup){
 
     when:
     params.do_dedup
+    
+    shell:
+    '''
+    samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | samtools view -bS -o !{file_id}_dedup.bam
+    input=$(samtools view -h !{bam[0]} | wc -l)
+    output=$(samtools view -h !{bam[0]} | awk '!seen[substr($1, length($1)-5) $3 $4 $10]++' | wc -l)
+    diff=$(($input - $output))
+    per=$(($diff * 100 / $input))
+    echo "Input : $input reads" > !{file_id}_dedup.log
+    echo "Output : $output reads" >> !{file_id}_dedup.log
+    echo "$per % duplicated reads" >> !{file_id}_dedup.log
+    '''
 
-    """
-    umi_tools dedup -I ${bam[0]} \
-    -S ${file_id}.dedup.bam \
-    > ${file_id}_dedup.log
-    """
   }
 } else {