diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index 4591b62a113..0037c1ef8ac 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -77,7 +77,7 @@
                     Line diffs are needed because cuffdiff does not produce deterministic output.
                     TODO: can we find datasets that lead to deterministic behavior?
                 -->
-                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/>
+                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/>
                 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/>
                 <output name="tss_groups_exp" file="cuffdiff_out3.txt"/>
                 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>