Mercurial > repos > jjohnson > defuse
comparison README @ 1:36306d8086fa
Remove defuse dir
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 16 Sep 2011 12:41:37 -0500 |
| parents | |
| children | 4245c2b047de |
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| 0:efddb7a0b3db | 1:36306d8086fa |
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| 1 The DeFuse galaxy tool is based on DeFuse_Version_0.4.2 | |
| 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_0.4.2 | |
| 9 | |
| 10 | |
| 11 The included defuse source code is from: http://sourceforge.net/projects/defuse/files/defuse/0.4/defuse-0.4.2.tar.gz/download | |
| 12 (without the defuse-0.4.2 dir level) | |
| 13 tar zxf defuse-0.4.2.tar.gz | |
| 14 cd tool | |
| 15 make | |
| 16 cd .. | |
| 17 | |
| 18 To use with non human genome references: | |
| 19 tar zxf modified_scripts.tgz | |
| 20 Defuse source was modified to include 2 extra parameters for non human references: gene_id_pattern and transcript_id_pattern | |
| 21 scripts/alignjob.pl | |
| 22 scripts/annotate_fusions.pl | |
| 23 scripts/calculate_expression_simple.pl | |
| 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 | |
| 28 | |
| 29 | |
| 30 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 | |
| 32 | |
| 33 |