FusionSeq

From GersteinInfo

(Difference between revisions)

Latest revision as of 11:43, 7 May 2011

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

@@ Line 1: / Line 1: @@
 <center>[http://rnaseq.gersteinlab.org/fusionseq/ FusionSeq main web page]</center>
-=Introduction=
+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.
-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|requirements]] '''before''' [[#Download|downloading]] FusionSeq.
-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.
-==Software Requirements==
-FusionSeq requires several additional packages to be installed in order to carry out the analysis and visualize the results. Moreover, since its modularity, different programs would need specific libraries. Moreover, some data set are also required for the analysis (see [[#Data Requirements|Data Requirements]]). Here we describe the complete set of tools that one would need to run the analysis as we do in our lab. The modules should be installed in the listed order.
-===Alignment tools===
+'''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.
-* [http://bowtie-bio.sourceforge.net/index.shtml bowtie] (64bit)
-* [http://users.soe.ucsc.edu/~kent/src/ Blat (source)] [http://genome-test.cse.ucsc.edu/~kent/exe/ (binaries)]
-Please make sure that blat and bowtie executables are part of the PATH, i.e. they can be accessed and executed from any location on your file system. Moreover, make sure that twoBit2fa is also downloaded from the blat package and part of the PATH.
-===Scientific and bioinformatics libraries===
-* [http://www.gnu.org/software/gsl/ GNU Scientific Library]
-* [http://rnaseq.gersteinlab.org/doc/bios/ BIOS]
-===Drawing tools===
+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]
-* [http://www.libgd.org/Main_Page GD library]
-===Data analysis===
-* [http://root.cern.ch/drupal/ ROOT]
-==Data Requirements==
+==[[FusionSeq Requirements]]==
+List of required programs and data. Please read this section '''before''' downloading FusionSeq.
-Here is the list of required data for a comprehensive use of FusionSeq tools.
+==[[FusionSeq Download|Download]]==
+Links to FusionSeq source code and data sets.
-===External===
+==[[Installation and Configuration of FusionSeq]]==
-*[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Homo Sapiens Reference genome (hg18)]: the user should download both chromFa.zip and hg18.2bit.
+Instructions to install and configure FusionSeq.
-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===
+==[[How to execute FusionSeq]]==
-The following data sets, bundled in a tarball, can be downloaded [http://rnaseq.gersteinlab.org/tarballs/FusionSeq_Annotation_Data_1.0.tar.gz here].
+An example workflow of FusionSeq.
-* knownGeneAnnotation.txt
-* knownGeneAnnotationTranscriptCompositeModel.txt
-* knownGeneAnnotationTranscriptCompositeModel.fa
-* kgXref.txt
-* knownToTreefam.txt
-The composite model needs to be indexed by bowtie:
+==[[FusionSeq_List of programs|List of programs]]==
- $ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa /path2bowtieIndex/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel
+Description of all the FusionSeq programs.
-Please make sure that the correct filenames are used.
+==[[FusionSeq_Test Datasets|Test Datasets]]==
+A few datasets to test FusionSeq installation.
-=[[Download]]=
+==[http://dynamic.gersteinlab.org/people/asboner/FusionSeq/geneFusions_cgi 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.
-=[[Installation and Configuration of FusionSeq]]=
+==[[FusionSeq_FAQ|Frequently Asked Questions (FAQ)]]==
+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]
-=[[How to execute FusionSeq]]=
+==[[FusionSeq Gallery|Gallery]]==
+Some figures about FusionSeq.
-{{FusionSeqFooter}}
+==[[FusionSeq_Papers|In the news et al.]]==
+News or scientific papers referring to FusionSeq

FusionSeq

From GersteinInfo

Latest revision as of 11:43, 7 May 2011

Contents

FusionSeq Requirements

Download

Installation and Configuration of FusionSeq

How to execute FusionSeq

List of programs

Test Datasets

Demo

Frequently Asked Questions (FAQ)

Gallery

In the news et al.

Views

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