diff --git a/IsoSCM/src/executable/IsoSCM.java b/IsoSCM/src/executable/IsoSCM.java
index 77519c3..1e8d937 100644
--- a/IsoSCM/src/executable/IsoSCM.java
+++ b/IsoSCM/src/executable/IsoSCM.java
@@ -218,7 +218,7 @@ else if(jc.getParsedCommand().equals("assemble")){
 				SAMFileReader sfr = new SAMFileReader(bamFile);
 				logger.info("tabulating splice junctions...");
 				BEDWriter sj_bw = new BEDWriter(IO.bufferedPrintstream(splice_junction_bed));
-				FindSpliceJunctions.tabulateSpliceJunctions(sfr, sj_bw);
+				FindSpliceJunctions.tabulateSpliceJunctions(sfr, strandedness, sj_bw);
 				sj_bw.close();
 
 				logger.info("counting junction supporting reads...");
diff --git a/IsoSCM/src/processing/FindSpliceJunctions.java b/IsoSCM/src/processing/FindSpliceJunctions.java
index fa5330d..9b1d634 100644
--- a/IsoSCM/src/processing/FindSpliceJunctions.java
+++ b/IsoSCM/src/processing/FindSpliceJunctions.java
@@ -114,7 +114,7 @@ public static List<AnnotatedRegion> splice_junctions(SAMRecord sr){
 		return splice_junctions;
 	}
 
-	public static StrandedGenomicIntervalTree<Map<String,Object>> tabulateSpliceJunctions(SAMFileReader sfr, BEDWriter bw){
+	public static StrandedGenomicIntervalTree<Map<String,Object>> tabulateSpliceJunctions(SAMFileReader sfr, Strandedness strandedness, BEDWriter bw){
 		Map<String,Integer> referenceLengths = BAMTools.referenceSequenceLengths(sfr.getFileHeader());
 
 		StrandedGenomicIntervalTree<Map<String,Object>> splice_junctions = new StrandedGenomicIntervalTree<Map<String,Object>>();
@@ -130,6 +130,9 @@ public static StrandedGenomicIntervalTree<Map<String,Object>> tabulateSpliceJunc
 				SAMRecord sr = sri.next();
 				if(sr.getCigarString().indexOf('N') == -1)
 					continue;
+				
+				if(strandedness!=Strandedness.unstranded && sr.getAttribute("XS")!=null && BAMTools.strand(sr, strandedness)!=sr.getCharacterAttribute("XS"))
+					continue;
 
 				Cigar cigar = sr.getCigar();
 				int alignmentPosition = sr.getAlignmentStart();
@@ -869,6 +872,9 @@ public MapCounter<Integer> instantiate(Object... objects) {
 			String chr = sr.getReferenceName();
 			int alignment_start = sr.getAlignmentStart();
 			
+			if(strandedness!=Strandedness.unstranded && sr.getAttribute("XS")!=null && BAMTools.strand(sr, strandedness)!=sr.getCharacterAttribute("XS"))
+				continue;
+			
 			if(prev_chr!=null && !chr.equals(prev_chr)){
 				writeAll(strand_count_5p_splice,strand_count_5p_span, prev_chr, true,gw);
 				// IMPORTANT: corrected error when last read aligned to the chromosome is spliced