# HG changeset patch
# User plus91-technologies
# Date 1403159383 14400
# Node ID da3c9b9fb9920b3e87b325e6db0a0093ff3f8a05
# Parent  2006814aa6f3489fa306f6836ba28b191a765fc6
Uploaded

diff -r 2006814aa6f3 -r da3c9b9fb992 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Thu Jun 19 02:29:43 2014 -0400
@@ -0,0 +1,49 @@
+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.
+
+ Google Code Link:
+ 
+		https://code.google.com/p/softsearch/
+		
+------------------------------------------------------------------------------------------------------------------		
+Pre-Requirement:
+
+ -Perl
+ -Bedtools  
+ -SamTools
+   Must have an entry in environment variable
+    
+------------------------------------------------------------------------------------------------------------------
+How To Selecte fasta file from Database (Additional Configuration):
+
+ --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>
+
+------------------------------------------------------------------------------------------------------------------
+Authors:
+
+   ResearchDx
+   http://researchdx.com
+   
+   Plus91 Technologies Private Limited
+   http://www.plus91.in/