Mercurial > repos > jjohnson > defuse
annotate README @ 2:4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
| author | Jim Johnson <jj@umn.edu> |
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| date | Tue, 08 Nov 2011 13:56:35 -0600 |
| parents | 36306d8086fa |
| children | 679a5c7b1294 |
| rev | line source |
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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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1 The DeFuse galaxy tool is based on DeFuse_Version_0.4.3 |
| 1 | 2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page |
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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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| 7 Manual: | |
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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
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8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.3 |
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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
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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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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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12 (to install uncompress the defuse source and navigate to the tools dir and type make) |
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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13 tar zxf defuse-0.4.3.tar.gz |
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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14 cd defuse-0.4.3/tool |
| 1 | 15 make |
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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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16 cd ../.. |
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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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18 Generate Reference Datasets as described in the Manual: |
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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19 |
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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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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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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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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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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22 |
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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23 These datasets should be referenced in the tool-data/defuse.loc file. |
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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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Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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27 and call defuse-0.4.3/scripts/defuse.pl |
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