--- a/README	Fri Sep 16 12:41:37 2011 -0500
+++ b/README	Tue Nov 08 13:56:35 2011 -0600
@@ -1,33 +1,29 @@
-The DeFuse galaxy tool is based on DeFuse_Version_0.4.2
+The DeFuse galaxy tool is based on DeFuse_Version_0.4.3
   http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
 
 DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.
 
 
 Manual:
-  http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
+  http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.3
 
 
-The included defuse source code is from: http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.2.tar.gz/download 
-(without the defuse-0.4.2 dir level)
-tar zxf defuse-0.4.2.tar.gz
-cd tool 
+The included defuse source code is from:   http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.3.tar.gz/download 
+(to install uncompress the defuse source and navigate to the tools dir and type make)
+tar zxf defuse-0.4.3.tar.gz
+cd defuse-0.4.3/tool 
 make
-cd ..
+cd ../..
 
-To use with non human genome references:
-tar zxf modified_scripts.tgz
-Defuse source was modified to include 2 extra parameters for non human references: gene_id_pattern and transcript_id_pattern
-	scripts/alignjob.pl
-	scripts/annotate_fusions.pl
-	scripts/calculate_expression_simple.pl
-	scripts/filter_bulk_fusion_reads.pl
-	scripts/filter_sam_genes.pl
-	scripts/find_concordant_ensembl.pl
-	scripts/find_gene_clusters.pl
+Generate Reference Datasets as described in the Manual: 
+
+  The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18.  
+  We were able to follow the same basic procedures to set up a reference for Mouse mm9.
+
+  These datasets should be referenced in the tool-data/defuse.loc file.   
 
 
 The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc
-and call scripts/defuse.pl
+and call defuse-0.4.3/scripts/defuse.pl