diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index fd2701caa82..9f4f7e72171 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -164,7 +164,7 @@
                 <output name="cds_diff" file="cuffdiff_out11.txt"/>
                 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
                 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
-                <output name="tss_groups_exp" file="cuffdiff_out3.txt"/>
+                <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
                 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
                 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
                 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>