diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index 764a52e07e3..68678863183 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -158,7 +158,6 @@
                 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
                 <!-- Defaults. -->
                 <param name="fdr" value="0.05" />
-                <param name="min_mapqual" value="0" ftype="sam" />
                 <param name="min_alignment_count" value="0" ftype="sam" />
                 <param name="do_bias_correction" value="No" />
                 <param name="do_normalization" value="No" />
diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index f54c906d9ea..538d1a5c1a1 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -109,7 +109,6 @@
             <param name="max_intron_len" value="300000"/>
             <param name="min_isoform_fraction" value="0.05"/>
             <param name="pre_mrna_fraction" value="0.05"/>
-            <param name="min_map_quality" value="0"/>
             <param name="use_ref" value="No"/>
             <param name="do_normalization" value="No" />
             <param name="do_bias_correction" value="No"/>