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DeFuse - Allow user to save the workspace, create an html file with links to the files in the workspace. Allow the creatation of an HTML formatted results.filtered.tsv with links to cluster detail provided by the get_read.pl command.
author Jim Johnson <jj@umn.edu>
date Fri, 06 Jan 2012 16:06:17 -0600
parents 4245c2b047de
children 679a5c7b1294
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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_0.4.3


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 ../..

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 defuse-0.4.3/scripts/defuse.pl