Fusionseq 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.
'''Note''': the following instructions apply if one wants to compile FusionSeq from the source code (all versions). Alternatively, one can download the FusionSeq_Download#Binaries (version 7.0 and later).
- [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 twoBitToFa is also downloaded from the blat package and part of the PATH.
- [http://www.gnu.org/software/gsl/ GNU Scientific Library (GSL)]: this library is a required for the compilation of [http://rnaseq.gersteinlab.org/doc/bios/ BIOS]. As a reference, we tested FusionSeq with gsl-1.14.
- Starting with version 0.7.0, two new libraries are required:
- [http://rnaseq.gersteinlab.org/doc/bios/ libbios], which replaces the old BIOS, can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libbios-1.1.0.tar.gz here].
- [http://rnaseq.gersteinlab.org/doc/mrf/ libmrf] can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libmrf-1.0.0.tar.gz here] Please note that this libraries are for the "early access" version of FusionSeq.
- [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] library: this library can be downloaded as part of [http://rseqtools.gersteinlab.org RSEQtools], a computational framework to analyze RNA-Seq data, or it can be downloaded as a separate component from [http://rnaseq.gersteinlab.org/fusionseq/tarballs/bios_0.9.0.tar.gz here].
Instructions to install [http://www.gnu.org/software/gsl/ GSL] and [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] (or libbios and libmrf -- depending on the version) can be found in '''Installation and Configuration of FusionSeq'''. However, please ensure that you read all the requirements (including #Data_requirements) and downloaded all the libraries and packages needed.
- [http://www.boutell.com/gd/ GD library]: The gd library is used to create schematic images of the PE reads connecting the two genes. It is required by FusionSeq_List_of_programs#gfr2images, which is an optional component of FusionSeq. As a reference, we tested FusionSeq with gd-2.0.35.
- [http://root.cern.ch/drupal/ ROOT]: this is a very powerful mathematical and computational framework. In the context of FusionSeq, it is used to perform a Kolomogorov-Smirnov analysis for filtering the breakpoint junctions and plotting the insert-size distribution.
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Here is the list of required data for a comprehensive use of FusionSeq tools.
- [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ 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 /path/to/bowtie/Index/hg18_nh/hg18_nh where '''hg18_nh.fa''' corresponds to the concatenation of all human chromosomes from chromFa.zip ''without'' the different haplotypes and the "random" sequences.
The following data sets (for hg18), bundled in a tarball, can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/FusionSeq_Annotation_Data_hg18_1.1.tar.gz here (hg18)]. For hg19 see #Human genome GRCh37/hg19.
- knownGeneAnnotationTranscriptCompositeModel.txt - the interval file with the coordinates of the composite models
- knownGeneAnnotationTranscriptCompositeModel.fa - the sequences 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
- ribosomal.2bit - the ribosomal sequences in 2bit format
The composite model needs to be indexed by bowtie: <pre> $ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa /path/to/bowtie/Index/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel </pre> knownGeneAnnotationTranscriptCompositeModel.txt (the interval file) and knownGeneAnnotationTranscriptCompositeModel.fa (the sequences) should be located in the same directory.
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.
The corresponding version of these files for hg19 can be found [http://rnaseq.gersteinlab.org/fusionseq/tarballs/FusionSeq_Annotation_Data_hg19_1.0.tar.gz here (hg19)].
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