From GersteinInfo

FusionSeq main web page

Contents 1 Introduction 1.1 Software Requirements 1.1.1 Alignment tools 1.1.2 Scientific and bioinformatics libraries 1.1.3 Drawing tools 1.1.4 Data analysis 1.2 Data Requirements 1.2.1 External 1.2.2 Provided 2 Download 3 Installation and Configuration of FusionSeq 4 How to execute FusionSeq 4.1 Troubleshooting

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

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). 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

• bowtie (64bit)
• Blat (source) (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

• GNU Scientific Library
• BIOS

Drawing tools

• GD library

Data analysis

• ROOT

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

Troubleshooting

Here are some common issues when installing FusionSeq and the associated libraries:

• libraries compiled for different architectures:

Make sure you installed and configured all libraries for the same architecture. For example, if you have a 64bit machine, use the flag CFLAGS=-m64 in the configure command.

• /usr/bin/ld: cannot find -lpng (or -ljpeg)

This usually occurs when compiling the optional program gfr2images which creates the schematic images of the connected exons between the two genes. You need to define the location of the libraries in the Makefile (see Auxilliary modules).