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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
author Jim Johnson <jj@umn.edu>
date Tue, 08 Nov 2011 13:56:35 -0600
parents 36306d8086fa
children 679a5c7b1294
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1:36306d8086fa 2:4245c2b047de
1 The DeFuse galaxy tool is based on DeFuse_Version_0.4.2 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 2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
3 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. 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_0.4.2 8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.3
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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 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 (without the defuse-0.4.2 dir level) 12 (to install uncompress the defuse source and navigate to the tools dir and type make)
13 tar zxf defuse-0.4.2.tar.gz 13 tar zxf defuse-0.4.3.tar.gz
14 cd tool 14 cd defuse-0.4.3/tool
15 make 15 make
16 cd .. 16 cd ../..
17 17
18 To use with non human genome references: 18 Generate Reference Datasets as described in the Manual:
19 tar zxf modified_scripts.tgz 19
20 Defuse source was modified to include 2 extra parameters for non human references: gene_id_pattern and transcript_id_pattern 20 The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18.
21 scripts/alignjob.pl 21 We were able to follow the same basic procedures to set up a reference for Mouse mm9.
22 scripts/annotate_fusions.pl 22
23 scripts/calculate_expression_simple.pl 23 These datasets should be referenced in the tool-data/defuse.loc file.
24 scripts/filter_bulk_fusion_reads.pl
25 scripts/filter_sam_genes.pl
26 scripts/find_concordant_ensembl.pl
27 scripts/find_gene_clusters.pl
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30 The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc 26 The defuse.xml galaxy tool wrapper will generate a defuse config.txt using values from tool-data/defuse.loc
31 and call scripts/defuse.pl 27 and call defuse-0.4.3/scripts/defuse.pl
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33 29