diff --git a/tools/ngs_rna/cuffdiff_wrapper.py b/tools/ngs_rna/cuffdiff_wrapper.py
index 64a0c0b337f..f263a8256c0 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.py
+++ b/tools/ngs_rna/cuffdiff_wrapper.py
@@ -57,7 +57,6 @@ def __main__():
     parser.add_option( '-m', '--inner-mean-dist', dest='inner_mean_dist', help='This is the expected (mean) inner distance between mate pairs. \
                                                                                 For, example, for paired end runs with fragments selected at 300bp, \
                                                                                 where each end is 50bp, you should set -r to be 200. The default is 45bp.')
-    parser.add_option( '-Q', '--min-mapqual', dest='min_mapqual', help='Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0.' )
     parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus\' observed changes don\'t contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' )
     parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' )
 
@@ -78,7 +77,7 @@ def __main__():
     parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" )
 
     # Bias correction options.
-    parser.add_option( '-r', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.')
+    parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.')
     parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
     parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
     parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
@@ -145,8 +144,6 @@ def __main__():
         cmd += ( " -p %i" % int ( options.num_threads ) )
     if options.inner_mean_dist:
         cmd += ( " -m %i" % int ( options.inner_mean_dist ) )
-    if options.min_mapqual:
-        cmd += ( " -Q %i" % int ( options.min_mapqual ) )
     if options.min_alignment_count:
         cmd += ( " -c %i" % int ( options.min_alignment_count ) )
     if options.FDR:
@@ -158,7 +155,7 @@ def __main__():
     if options.do_normalization:
         cmd += ( " -N" )
     if options.do_bias_correction:
-        cmd += ( " -r %s" % seq_path )
+        cmd += ( " -b %s" % seq_path )
             
     # Add inputs.
     # For replicate analysis: group1_rep1,group1_rep2 groupN_rep1,groupN_rep2
diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index f9500e145d2..835eb369c46 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -7,7 +7,6 @@
         cuffdiff_wrapper.py
             --FDR=$fdr
             --num-threads="4"
-            --min-mapqual=$min_mapqual
             --min-alignment-count=$min_alignment_count
 
             --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking
@@ -36,7 +35,7 @@
             
             ## Bias correction?
             #if $bias_correction.do_bias_correction == "Yes":
-	        -r
+	        -b
                 #if $bias_correction.seq_source.index_source == "history":
                     --ref_file=$bias_correction.seq_source.ref_file
                 #else:
@@ -97,7 +96,6 @@
         </conditional>
 
         <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
-        <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/>
         <param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
         <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>
@@ -169,8 +167,8 @@
                     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="14"/>
-                <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="10"/>
+                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="56"/>
+                <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="30"/>
                 <output name="tss_groups_exp" file="cuffdiff_out3.txt"/>
                 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
                 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="16"/>
@@ -238,7 +236,6 @@ This is a list of implemented Cuffdiff options::
 
   -m INT                         This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp.
   -s INT                         The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
-  -Q	                         Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0.
   -c INT                         The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).
   --FDR FLOAT                    The allowed false discovery rate. The default is 0.05.
   --num-importance-samples INT   Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000
diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index 59cdfdc7ef4..b70d740eb51 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -209,7 +209,6 @@ This is a list of implemented Cufflinks options::
   -I INT    The minimum intron length. Cufflinks will not report transcripts with introns longer than this, and will ignore SAM alignments with REF_SKIP CIGAR operations longer than this. The default is 300,000.
   -F 	    After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene.
   -j        Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%.
-  -Q	    Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0.
   -G	    Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.  
   -N        With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.
     </help>