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Update create_reference_dataset for non human genome builds
author Jim Johnson <jj@umn.edu>
date Sat, 15 Jun 2013 14:36:47 -0500
parents 06675bd664ee
children 225750bf3770
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17:fc35b7b993b1 18:547d8db4673e
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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. 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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7 Manual: 7 Manual:
8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.0 8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
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10 The included tool_dependencies.xml will download and install the defuse code. 10 The included tool_dependencies.xml will download and install the defuse code.
11 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install. 11 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install.
12 The tool_dependencies.xml also has the download for bowtie. 12 The tool_dependencies.xml also has the download for bowtie.
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32 The create_reference_dataset.pl script will download the genome and other source files, and build any derivative files including bowtie indices, gmap indices, and 2bit files. Run the following command. Expect this step to take at least 12 hours. 32 The create_reference_dataset.pl script will download the genome and other source files, and build any derivative files including bowtie indices, gmap indices, and 2bit files. Run the following command. Expect this step to take at least 12 hours.
33 create_reference_dataset.pl -c config.txt 33 create_reference_dataset.pl -c config.txt
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35 These datasets should be referenced in the tool-data/defuse.loc file. 35 These datasets should be referenced in the tool-data/defuse.loc file.
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37 The create_reference_dataset will run the create_reference_dataset.pl script to generate deFuse genome reference data in a galaxy dataset.
38 This should me made available in the future as a Galaxy DataManager.
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38 Galaxy will try to auto-install dependencies: 41 Galaxy will try to auto-install dependencies:
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40 External Tools ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1 ) 43 External Tools ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1 )
41 deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below. 44 deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below.