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1 The DeFuse galaxy tool is based on DeFuse_Version_0.4.2
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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_0.4.2
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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-0.4.2.tar.gz/download
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12 (without the defuse-0.4.2 dir level)
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13 tar zxf defuse-0.4.2.tar.gz
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14 cd tool
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15 make
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16 cd ..
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17
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18 To use with non human genome references:
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19 tar zxf modified_scripts.tgz
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20 Defuse source was modified to include 2 extra parameters for non human references: gene_id_pattern and transcript_id_pattern
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21 scripts/alignjob.pl
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22 scripts/annotate_fusions.pl
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23 scripts/calculate_expression_simple.pl
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24 scripts/filter_bulk_fusion_reads.pl
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25 scripts/filter_sam_genes.pl
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26 scripts/find_concordant_ensembl.pl
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27 scripts/find_gene_clusters.pl
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28
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29
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30 The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc
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31 and call scripts/defuse.pl
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