From 633c3cb9d51b2fed5c6b6a23a35cb073d3e34d14 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 28 Apr 2012 22:21:30 -0400
Subject: [PATCH] Update Cuffdiff min-alignment-count default.

---
 tools/ngs_rna/cuffdiff_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index b75622ddf61..7fc1bfb857a 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -89,7 +89,7 @@
         </conditional>
 
         <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
-        <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="min_alignment_count" type="integer" value="10" 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>
             <option value="Yes">Yes</option>