diff --git a/src/bin/friends_emma.rs b/src/bin/friends_emma.rs
index 7b0eaa9a..306e952b 100644
--- a/src/bin/friends_emma.rs
+++ b/src/bin/friends_emma.rs
@@ -142,7 +142,18 @@ fn main(){
             qual_cigar.push(qual_recalc_char);
         }
 
-        println!("@{}\n{}\n+\n{}",seq_counter,seq,qual_cigar);
+        if paired_end {
+            // split the seq and qual for paired end
+            let separator_pos = seq.find(READ_SEPARATOR).expect("ERROR finding read separator");
+            let r1_seq = seq[0..separator_pos].to_string();
+            let r2_seq = seq[separator_pos+1..].to_string();
+            let r1_qual= qual_cigar[0..separator_pos].to_string();
+            let r2_qual= qual_cigar[separator_pos+1..].to_string();
+            println!("@{}/1\n{}\n+\n{}",seq_counter,r1_seq,r1_qual);
+            println!("@{}/2\n{}\n+\n{}",seq_counter,r2_seq,r2_qual);
+        } else {
+            println!("@{}\n{}\n+\n{}",seq_counter,seq,qual_cigar);
+        }
     }
 }
 
diff --git a/tests/friends_emma.sh b/tests/friends_emma.sh
index 95885aee..e9286e3b 100644
--- a/tests/friends_emma.sh
+++ b/tests/friends_emma.sh
@@ -22,4 +22,16 @@ if [ "$total_quals" != "259.31" ]; then
   exit 1
 fi
 
+pe_collapsed=$(cat $INPUT $INPUT $INPUT | ./target/debug/friends_emma --paired-end | ./target/debug/friends_rachel --each-read)
+IDs=$(echo "$pe_collapsed" | cut -f 1 | tail -n +2 | paste -sd+)
+pe_quals=$(echo "$pe_collapsed" | cut -f 3 | tail -n +2 | paste -sd+ | bc -l)
+if [ "$IDs" != "1/1+1/2+2/1+2/2+3/1+3/2+4/1+4/2" ]; then
+  echo "Test failed for total expected quality when collapsing three sets of reads using --paired-end"
+  exit 1
+fi
+if [ "$total_quals" != "$pe_quals" ]; then
+  echo "Test failed for having the same quality scores in SE mode as PE mode"
+  exit 1
+fi
+
 echo "$0 passed";