diff --git a/src/HMCan b/src/HMCan
index dd21276..d2921c4 100755
Binary files a/src/HMCan and b/src/HMCan differ
diff --git a/src/Profiler.cpp b/src/Profiler.cpp
index 5d36a9f..0deb928 100644
--- a/src/Profiler.cpp
+++ b/src/Profiler.cpp
@@ -237,7 +237,7 @@ void Profiler::build_single_profile(vector<DNA_fragment >& tags, string chr, boo
         }
 	}
 
-	if (pairedEnds_) { //divide density by 2 for PE datasets:
+	if (pairedEnds_ && isChIPseq_) { //divide density by 2 for PE datasets:
         for(int i=0;i<sampled_sizes[chr];i++){
             if(targetORcontrol)
                 sampled_target_density[chr][i] =sampled_target_density[chr][i]/2.0;
diff --git a/src/main.cpp b/src/main.cpp
index 367da72..3dea66a 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -30,7 +30,7 @@ using namespace std;
 #include"Reader.h"
 #include "HMCan.h"
 #include "Parser.h"
-const double HMCAN_VERSION = 1.41;
+const double HMCAN_VERSION = 1.42;
 
 static void print_version()
 {