# HG changeset patch
# User plus91-technologies
# Date 1402322327 14400
# Node ID 92d8479f1616d6c8c4863a9027ab798856f97b1e
# Parent  06e32c8b56823a9bef59ad225afbf519f88ed875
Uploaded

diff -r 06e32c8b5682 -r 92d8479f1616 README 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README 	Mon Jun 09 09:58:47 2014 -0400
@@ -0,0 +1,36 @@
+1.SoftSearch:
+
+ --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in 
+   illumina next-generation sequencing data. 
+
+ --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.
+
+ --Breakpoint is a place or time at which an interruption or change is made.
+
+ --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned.
+
+ 	
+2.Setting for selecting fasta file from database.
+
+ --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
+   8578d978014c/softsearch/tool-data/
+
+ --open the fasta_indexes.loc file and make changes like
+
+        <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+
+        eg: hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
+
+ --open shed_tool_data_table_conf.xml file and add following.
+
+   	<tables>
+	    <table name="fasta_indexes" comment_char="#">
+      	    <columns>value, dbkey, name, path</columns>
+       	    <file path="/path/to/fasta_indexes.loc" />
+  	    </table>
+	</tables>
+
+
+Notes:
+  --Need latest version of Samtools(version above 0.1.18) and perl installed on local system.
+