diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index 16e697dfb31fff467feec82fd2375a1ca243650f..8ce498c17876097be421ba7294c921f42c774093 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -231,7 +231,7 @@ fi
 for bamFile in $bamFiles; do
     sample=$(basename $bamFile .bam)
     echo "converting $bamFile to bigwig format"
-    mysub "${project}__bw__${sample}" "genomeCoverageBed -bg -ibam $bamFile  -g ${genomeFai} |  wigToBigWig -clip stdin ${genomeFai} ${sample}.bw" -q short | joblist .bigwig
+    mysub "${project}__bw__${sample}" "genomeCoverageBed -split -bg -ibam $bamFile  -g ${genomeFai} |  wigToBigWig -clip stdin ${genomeFai} ${sample}.bw" -q short | joblist .bigwig
 done
 
 wait4jobs .bigwig