FusionSeq
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Introduction
This page provides the source code for FusionSeq. Please note that these tools were tested on a multi-node cluster of computing nodes with Linux Red Hat as operating system and PBS as scheduler system. FusionSeq programs are written in C and should likely compile to most Unix/Linux platforms. We used the gcc complier (version 3.4.6 20060404) to compile the source code. However, this is not a plug-and-play program, but it requires the user to compile, install and run a set of programs. Please read the requirements before downloading FusionSeq.
Software Requirements
Data Requirements
Here is the list of required data for a comprehensive use of FusionSeq tools.
External
- Homo Sapiens Reference genome (hg18): the user should download both chromFa.zip and hg18.2bit.
The human genome needs to be properly indexed to be used by bowtie. Please see the instruction of bowtie for performing this operation. Indicatevely, you would need to run something like:
$ bowtie-build -f hg18_nh.fa /path2bowtieIndex/hg18_nh/
where hg18_nh.fa corresponds to the concatenation of all human chromosomes from chromFa.zip without the different haplotypes and "random" stuff.
Provided
The following data sets, bundled in a tarball, can be downloaded here.
- knownGeneAnnotation.txt
- knownGeneAnnotationTranscriptCompositeModel.txt
- knownGeneAnnotationTranscriptCompositeModel.fa
- kgXref.txt
- knownToTreefam.txt
The composite model needs to be indexed by bowtie:
$ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa /path2bowtieIndex/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel
Please make sure that the correct filenames are used.
Download
Installation and Configuration of FusionSeq
How to execute FusionSeq
last revision: 12:53, 19 August 2010 (UTC)
