diff --git a/pipeline/transcriptome.py b/pipeline/transcriptome.py
index 65925ea..a1dd12f 100644
--- a/pipeline/transcriptome.py
+++ b/pipeline/transcriptome.py
@@ -346,7 +346,7 @@ def htseq_to_matrix(self):
                         else:
                             values.append('0')
                     if all([x not in gene_id for x in bad_fields]):
-                        print(gene_id + '\t' + '\t'.join(values), file=f_out)
+                        print(gene_id.strip() + '\t' + '\t'.join(values), file=f_out)
 
             print("Done\n\n")