Mercurial > repos > plus91-technologies > softsearch

changeset 29:79f80a903c8f draft default tip

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Uploaded
author plus91-technologies
date Thu, 19 Jun 2014 02:43:07 -0400
parents da3c9b9fb992
children
files README
diffstat 1 files changed, 11 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/README	Thu Jun 19 02:29:43 2014 -0400
+++ b/README	Thu Jun 19 02:43:07 2014 -0400
@@ -1,10 +1,11 @@
 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.
+ --SoftSearch is a tool that uses soft-masked reads and discordant read pairs to identify structural variants(SV) in 
+   Illumina paired-end next-generation sequencing data. 
+ --Using Soft Clipped reads in which one part of the read maps to the reference genome but the other part does not SoftSearch 
+   can identify and call SVs including deletions, insertions, translocations, inversions, and tandem duplications
+ --SoftSearch requires two inputs: a BAM file of aligned reads and fasta file of the reference genome to which the reads 
+   were aligned.
 
  Google Code Link:
  
@@ -16,21 +17,21 @@
  -Perl
  -Bedtools  
  -SamTools
-   Must have an entry in environment variable
+   Must be accessible from the PATH environment variable
     
 ------------------------------------------------------------------------------------------------------------------
-How To Selecte fasta file from Database (Additional Configuration):
+How To Select 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/
+ --A fasta_indexes.loc file must be located in 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
+ --open the fasta_indexes.loc file and add an entry according to the example below
 
         <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.
+ --open shed_tool_data_table_conf.xml file and add the following
 
    	<tables>
     <table name="fasta_indexes" comment_char="#">