FusionSeq

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<center>[http://rnaseq.gersteinlab.org/fusionseq/ FusionSeq main web page]</center>
<center>[http://rnaseq.gersteinlab.org/fusionseq/ FusionSeq main web page]</center>
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=Introduction=
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This document provides the information for downloading, installing, compile and run 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.  
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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.  
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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|requirements]] '''before''' [[#Download|downloading]] FusionSeq.
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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 [[#Download|downloading]] FusionSeq.
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==[[Software Requirements]]==
 
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==Data Requirements==
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'''IMPORTANT''': Starting from version 0.7.0, we adopted a different approach to include the configuration file that allows the users to simply download the binary files for their platform. However, we still provide the source code, which now uses the more standard autoconf/automake tools, thus simplifying the installation of FusionSeq. Please note that at the time of writing (May 7th, 2011), version 0.7.0 is still in alpha. Any feedback will be very much appreciated.
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Here is the list of required data for a comprehensive use of FusionSeq tools.
 
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===External===
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If you have any questions, please check the [[FusionSeq_FAQ|FAQ]] or send an email to [mailto:fusionseq-faq@gersteinlab.org fusionseq-faq@gersteinlab.org]
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*[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Homo Sapiens Reference genome (hg18)]: the user should download both chromFa.zip and hg18.2bit.
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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:  
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$ bowtie-build -f hg18_nh.fa /path2bowtieIndex/hg18_nh/
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where hg18_nh.fa corresponds to the concatenation of all human chromosomes from chromFa.zip without the different haplotypes and "random" stuff.
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===Provided===
 
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The following data sets, bundled in a tarball, can be downloaded [http://rnaseq.gersteinlab.org/tarballs/FusionSeq_Annotation_Data_1.0.tar.gz here].
 
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* knownGeneAnnotation.txt
 
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* knownGeneAnnotationTranscriptCompositeModel.txt
 
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* knownGeneAnnotationTranscriptCompositeModel.fa
 
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* kgXref.txt
 
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* knownToTreefam.txt
 
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The composite model needs to be indexed by bowtie:
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==[[FusionSeq Requirements]]==
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$ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa /path2bowtieIndex/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel
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List of required programs and data. Please read this section '''before''' downloading FusionSeq.
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Please make sure that the correct filenames are used.
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==[[FusionSeq Download|Download]]==
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Links to FusionSeq source code and data sets.
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=[[Download]]=
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==[[Installation and Configuration of FusionSeq]]==
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Instructions to install and configure FusionSeq.
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=[[Installation and Configuration of FusionSeq]]=
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==[[How to execute FusionSeq]]==
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An example workflow of FusionSeq.
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=[[How to execute FusionSeq]]=
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==[[FusionSeq_List of programs|List of programs]]==
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Description of all the FusionSeq programs.
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{{FusionSeqFooter}}
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==[[FusionSeq_Test Datasets|Test Datasets]]==
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A few datasets to test FusionSeq installation.
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==[http://dynamic.gersteinlab.org/people/asboner/FusionSeq/geneFusions_cgi Demo]==
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You can see some of the results of FusionSeq as described in the paper. Use the sample IDs reported in Table 1, e.g. 106_T, 1700_D.
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==[[FusionSeq_FAQ|Frequently Asked Questions (FAQ)]]==
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Solutions to common problems. If your issue is not described in the [[FusionSeq_FAQ|FAQ]], please send an email to [mailto:fusionseq-faq@gersteinlab.org fusionseq-faq@gersteinlab.org]
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==[[FusionSeq Gallery|Gallery]]==
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Some figures about FusionSeq.
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==[[FusionSeq_Papers|In the news et al.]]==
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News or scientific papers referring to FusionSeq

Latest revision as of 11:43, 7 May 2011

FusionSeq main web page

This document provides the information for downloading, installing, compile and run 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.


IMPORTANT: Starting from version 0.7.0, we adopted a different approach to include the configuration file that allows the users to simply download the binary files for their platform. However, we still provide the source code, which now uses the more standard autoconf/automake tools, thus simplifying the installation of FusionSeq. Please note that at the time of writing (May 7th, 2011), version 0.7.0 is still in alpha. Any feedback will be very much appreciated.


If you have any questions, please check the FAQ or send an email to fusionseq-faq@gersteinlab.org


Contents

FusionSeq Requirements

List of required programs and data. Please read this section before downloading FusionSeq.

Download

Links to FusionSeq source code and data sets.

Installation and Configuration of FusionSeq

Instructions to install and configure FusionSeq.

How to execute FusionSeq

An example workflow of FusionSeq.

List of programs

Description of all the FusionSeq programs.

Test Datasets

A few datasets to test FusionSeq installation.

Demo

You can see some of the results of FusionSeq as described in the paper. Use the sample IDs reported in Table 1, e.g. 106_T, 1700_D.

Frequently Asked Questions (FAQ)

Solutions to common problems. If your issue is not described in the FAQ, please send an email to fusionseq-faq@gersteinlab.org

Gallery

Some figures about FusionSeq.

In the news et al.

News or scientific papers referring to FusionSeq

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