FusionSeq Requirements

From GersteinInfo

Revision as of 20:07, 19 August 2010

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 sets 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 twoBitToFa 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.

• knownGeneAnnotationTranscriptCompositeModel.txt - the interval file with the coordinates of the composite models
• knownGeneAnnotationTranscriptCompositeModel.fa - the sequence of all the composite transcripts
• kgXref.txt - the mapping between the UCSC knownGene annotation set and other information (RefSeq, gene symbols and description etc.)
• knownToTreefam.txt - the mapping between UCSC knownGene annotation and TreeFam
• hg18_repeatMasker.interval - the interval file, i.e. the file with the coordinates, of the repetitive regions.

The composite model needs to be indexed by bowtie:

$ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa /path2bowtieIndex/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel

Although we extensively used the UCSC knownGene annotation set, it is worth mentioning that it is possible to use other gene annotation sets. However, in this case, the same information, and in the same format, should be provided to the corresponding programs.