| deFuse - gene fusion discovery using RNA-Seq data 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. http://sourceforge.net/apps/mediawiki/defuse/ https://bitbucket.org/dranew/defuse |
hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/defuse
| Name | Version | Type | |
|---|---|---|---|
| R | 3.1.2 | package | |
| ada | 2.0.3 | package | |
| blat | 35x1 | package | |
| bowtie | 1.0.0 | package | |
| defuse | 0.6.2 | package | |
| faToTwoBit | 35x1 | package | |
| gmap | 2013-05-09 | package | |
| samtools | 0.1.19 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| identify fusion transcripts | 0.6.2.2 | 16.01 | |
| generate a VCF from a DeFuse Results file | 0.6.2.2 | 16.01 | |
| converts a bam file to fastq files. | 0.6.2.2 | 16.01 | |
| create a defuse reference from Ensembl and UCSC sources | 0.6.2.2 | 16.01 | |
| create a defuse reference from Ensembl and UCSC sources | 0.6.2.2 | 16.01 | |
| verify fusions with trinity | 0.6.2.2 | 16.01 | |
| Name | Version | Data Tables |
|---|---|---|
| data_manager_defuse_reference | 0.0.1 | defuse_reference |
| extension | type | mimetype | subclass |
|---|---|---|---|
| defuse.conf | galaxy.datatypes.data:Text | True | |
| defuse.results.tsv | galaxy.datatypes.tabular:Tabular | True | |