Mercurial > repos > nate > nate_test
comparison README @ 2:999746fc92ba default tip
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| author | nate |
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| date | Thu, 10 Nov 2011 09:56:05 -0500 |
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| 1:ad220f659249 | 2:999746fc92ba |
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| 1 The DeFuse galaxy tool is based on DeFuse_Version_0.4.3 | |
| 2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | |
| 3 | |
| 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. | |
| 5 | |
| 6 | |
| 7 Manual: | |
| 8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.3 | |
| 9 | |
| 10 | |
| 11 The included defuse source code is from: http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.3.tar.gz/download | |
| 12 (to install uncompress the defuse source and navigate to the tools dir and type make) | |
| 13 tar zxf defuse-0.4.3.tar.gz | |
| 14 cd defuse-0.4.3/tool | |
| 15 make | |
| 16 cd ../.. | |
| 17 | |
| 18 Generate Reference Datasets as described in the Manual: | |
| 19 | |
| 20 The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18. | |
| 21 We were able to follow the same basic procedures to set up a reference for Mouse mm9. | |
| 22 | |
| 23 These datasets should be referenced in the tool-data/defuse.loc file. | |
| 24 | |
| 25 | |
| 26 The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc | |
| 27 and call defuse-0.4.3/scripts/defuse.pl | |
| 28 | |
| 29 |