diff --git a/.gitignore b/.gitignore
index 2404b8a..9f0a757 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,13 @@
 cpu.pprof
 cpu.trace
-obicount
-obipairing
 test
 bin
 vendor
 *.fastq
 *.fasta
-obiconvert
-obipcr
+
+/obiconvert
+/obicount
+/obimultiplex
+/obipairing
+/obipcr
diff --git a/pkg/obiseq/subseq.go b/pkg/obiseq/subseq.go
index 9571b1d..bdf353d 100644
--- a/pkg/obiseq/subseq.go
+++ b/pkg/obiseq/subseq.go
@@ -27,11 +27,20 @@ func (sequence BioSequence) Subsequence(from, to int, circular bool) (BioSequenc
 		newSeq = MakeEmptyBioSequence()
 		newSeq.Write(sequence.Sequence()[from:to])
 
+		if sequence.HasQualities() {
+			newSeq.WriteQualities(sequence.Qualities()[from:to])
+		}
+
 		newSeq.sequence.id = fmt.Sprintf("%s_sub[%d..%d]", sequence.Id(), from+1, to)
 		newSeq.sequence.definition = sequence.sequence.definition
 	} else {
 		newSeq, _ = sequence.Subsequence(from, sequence.Length(), false)
 		newSeq.Write(sequence.Sequence()[0:to])
+
+		if sequence.HasQualities() {
+			newSeq.WriteQualities(sequence.Qualities()[0:to])
+		}
+
 	}
 
 	if len(sequence.Annotations()) > 0 {