diff --git a/tools/ngs_rna/tophat2_wrapper.py b/tools/ngs_rna/tophat2_wrapper.py
index 7ccf8d5ce2b..1d7092987b9 100644
--- a/tools/ngs_rna/tophat2_wrapper.py
+++ b/tools/ngs_rna/tophat2_wrapper.py
@@ -64,6 +64,12 @@ def __main__():
     parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' )
     parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' )
     
+    # Bowtie2 options.
+    parser.add_option( '', '--b2-very-fast', action='store_true', dest='b2_very_fast')
+    parser.add_option( '', '--b2-fast', action='store_true', dest='b2_fast')
+    parser.add_option( '', '--b2-very-sensitive', action='store_true', dest='b2_very_sensitive')
+    parser.add_option( '', '--b2-sensitive', action='store_true', dest='b2_sensitive')
+    
     # Fusion search options.
     parser.add_option( '', '--fusion-search', action='store_true', dest='fusion_search' )
     parser.add_option( '', '--fusion-anchor-length', dest='fusion_anchor_length' )
@@ -198,6 +204,16 @@ def __main__():
                           ( int( options.fusion_anchor_length ), int( options.fusion_min_dist ),
                             int( options.fusion_read_mismatches ), int( options.fusion_multireads ),
                             int( options.fusion_multipairs ), options.fusion_ignore_chromosomes )
+                            
+            # Bowtie2 options.
+            if options.b2_very_fast:
+                opts += ' --b2-very-fast'
+            if options.b2_fast:
+                opts += ' --b2-fast'
+            if options.b2_sensitive:
+                opts += ' --b2-sensitive'
+            if options.b2_very_sensitive:
+                opts += ' --b2-very-sensitive'
                                         
             cmd = cmd % ( opts, index_path, reads )
             
diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml
index 47b98a11284..69d0b37c934 100644
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -105,6 +105,13 @@
                 --fusion-multipairs $params.fusion_search.multipairs
                 --fusion-ignore-chromosomes $params.fusion_search.ignore_chromosomes
             #end if
+            
+            #if $params.bowtie2_settings.b2_settings == "Yes":
+                #if $params.bowtie2_settings.preset.b2_preset == "Yes":
+                    --b2-$params.bowtie2_settings.preset.b2_preset_select
+                #end if    
+            #end if
+                        
         #end if
     </command>
     <inputs>
@@ -257,6 +264,33 @@
                       <param name="ignore_chromosomes" type="text" value='' label="Ignore some chromosomes such as chrM when detecting fusion break points"/>
                   </when>
               </conditional>
+              
+              <!-- Bowtie2 settings. -->
+              <conditional name="bowtie2_settings">
+                  <param name="b2_settings" type="select" label="Set Bowtie2 settings">
+                        <option selected="true" value="No">No</option>
+                        <option value="Yes">Yes</option>
+                  </param>
+                  <when value="No" />
+                  <when value="Yes">
+                      <conditional name="preset">
+                          <param name="b2_preset" type="select" label="Use Preset options">
+                                <option selected="true" value="Yes">Yes</option>
+                                <option value="No">No</option>
+                          </param>
+                          <when value="Yes">
+                              <param name="b2_preset_select" type="select" label="Preset option">
+                                  <option value="very-fast">Very fast</option>
+                                  <option selected="true" value="fast">Fast</option>
+                                  <option value="sensitive">Sensitive</option>
+                                  <option value="very-sensitive">Very sensitive</option>
+                              </param>
+                          </when>
+                          <!-- TODO: -->
+                          <when value="No" />
+                      </conditional>
+                  </when>
+              </conditional>
             </when>  <!-- full -->
       </conditional>  <!-- params -->
     </inputs>