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1 The DeFuse galaxy tool is based on DeFuse_Version_0.4.3
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2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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3
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4 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.
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6
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7 Manual:
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8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.3
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9
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10
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11 The included defuse source code is from: http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.3.tar.gz/download
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12 (to install uncompress the defuse source and navigate to the tools dir and type make)
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13 tar zxf defuse-0.4.3.tar.gz
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14 cd defuse-0.4.3/tool
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15 make
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16 cd ../..
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17
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18 Generate Reference Datasets as described in the Manual:
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19
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20 The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18.
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21 We were able to follow the same basic procedures to set up a reference for Mouse mm9.
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22
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23 These datasets should be referenced in the tool-data/defuse.loc file.
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24
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26 The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc
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27 and call defuse-0.4.3/scripts/defuse.pl
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