diff --git a/sinto/filterbarcodes.py b/sinto/filterbarcodes.py
index 3309b06..df31ba7 100644
--- a/sinto/filterbarcodes.py
+++ b/sinto/filterbarcodes.py
@@ -33,6 +33,9 @@ def _iterate_reads(
     bamlist = [pysam.AlignmentFile(x, filemode, header=newhead) for x in filelist]
     for i in intervals:
         for r in inputBam.fetch(i[0], i[1], i[2]):
+            # skip reads owned by the previous chunk (fetch returns overlaps); unmapped reads have reference_start < 0
+            if r.reference_start >= 0 and r.reference_start < i[1]:
+                continue
             if readname_barcode is not None:
                 re_match = readname_barcode.search(r.qname)
                 cell_barcode = re_match.group()