diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index 3b3cf0b5105..98daba8881f 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -52,8 +52,8 @@
     <inputs>
         <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
         <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/>
-        <param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/>
-        <param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" help=""/>
+        <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help=""/>
+        <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help=""/>
         <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
             <option value="No">No</option>
             <option value="Yes">Yes</option>