--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Sep 16 12:41:37 2011 -0500
@@ -0,0 +1,33 @@
+The DeFuse galaxy tool is based on DeFuse_Version_0.4.2
+  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
+
+
+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 
+make
+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
+
+
+The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc
+and call scripts/defuse.pl
+
+