diff --git a/Makefile b/Makefile
index 2d56d7c..8c73412 100644
--- a/Makefile
+++ b/Makefile
@@ -14,7 +14,9 @@ PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcrip
 
 all : $(PROGRAMS)
 
-$(SAMLIBS) :
+$(SAMTOOLS)/libbam.a : $(SAMTOOLS)/$(HTSLIB)/libhts.a
+
+$(SAMTOOLS)/$(HTSLIB)/libhts.a : 
 	cd $(SAMTOOLS) ; ${MAKE} all
 
 Transcript.h : utils.h
@@ -151,5 +153,6 @@ ebseq :
 
 clean :
 	rm -f *.o *~ $(PROGRAMS)
-	cd $(SAMTOOLS) ; ${MAKE} clean
+	cd $(SAMTOOLS) ; ${MAKE} clean 
+	rm -f $(SAMLIBS)
 	cd EBSeq ; ${MAKE} clean
diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index 008fa9a..8309614 100644
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,6 +1,7 @@
 RSEM v1.2.28
 
 - Fixed a bug in RSEM v1.2.27 that can lead to assertion errors for parsing GTF files
+- Fixed a bug in Makefile
 
 --------------------------------------------------------------------------------------------