diff --git a/4. DA Analyses/@kalmanFilter/run.m b/4. DA Analyses/@kalmanFilter/run.m
index 90ca87de..fcd81b19 100644
--- a/4. DA Analyses/@kalmanFilter/run.m	
+++ b/4. DA Analyses/@kalmanFilter/run.m	
@@ -15,6 +15,9 @@
 %
 %   Adev - Updated ensemble deviations (nState x nEns x nTime)
 %
+%   Aperc - Percentiles of the updated ensemble (nState x nPercentile x nTime)
+%           (See output.settings for the percentiles calculated) 
+%
 %   Ye - Proxy estimates
 %           Joint Updates:  (nObs x nEns)
 %           Serial Updates: (nObs x nEns x nTime)
@@ -69,7 +72,7 @@
     F = obj.adjustH( F, reconstruct );
     
     % Do the updates
-    output = obj.serialENSRF( M, obj.D, obj.R, F, w, obj.fullDevs );
+    output = obj.serialENSRF( M, obj.D, obj.R, F, w, obj.fullDevs, obj.percentiles );
     
     % Unappend if necessary
     output.Append = false;
@@ -84,7 +87,7 @@
     
     % Default localization
     if isempty(obj.localize)
-        w = ones( sum(obj.reconstruct), nObs);
+        w = ones( sum(reconstruct), nObs);
         yloc = ones( nObs, nObs);
     else
         w = obj.localize{1};
@@ -92,7 +95,7 @@
     end
         
     % Do the updates
-    output = obj.jointENSRF( M, obj.D, obj.R, obj.F, w, yloc, obj.meanOnly, obj.fullDevs, reconstruct );
+    output = obj.jointENSRF( M, obj.D, obj.R, obj.F, w, yloc, obj.meanOnly, obj.fullDevs, obj.percentiles, reconstruct );
 end
 
 end
\ No newline at end of file