Simulator Usage

Installation

The Flux Simulator executables do (in contrast to the Flux Capacitor) not depend on any system-specific code, it can be run straight away after downloading, un-zipping and de-tarring. However, file paths in the parameter files are absolute - othewise it would be very hard to allow for different locations of for instance the reference annotation file and the project files.

Therefore, when updating the demonstration files, please put them in the demo folder of your FluxSimulator installation directory, and subsequently call

./bin/sim.sh --install

to replace the corresponding absolute paths with the ones of your folder structure. The shell script sim.sh corresponding your platform should be used, sim.bat on windows or sim.command on Mac OSX. If everything is fine, the Simulator will tell you something along the lines of

[msammeth@mar Simulator]$ FluxSimulator-v1.2-j1.5/bin/sim.sh --install
[INIT] installing..
        wrote 30 lines to testRun.par
        [OK]

The Graphical User Interface (GUI)

Parameter Argument Modality Description
[-X|-gui|--graphical] mandatory start graphical user interface (GUI)
[-p|-par|--parameter] String optional specify parameter file (PAR file)

Examples

  • The standard program call for launching the GUI would be
sim -X
  • The following command would additionally load the parameters from a the parameter file test.par upon startup
sim -Xp test.par

The Command Line Interface

Parameter Argument Modality Description
[-p|-par|--parameter] String mandatory specify parameter file (PAR file)
[-x|-expr|--express] optional simulate expression
[-l|-lib|--library] optional simulate library construction
[-s|-seq|--sequence] optional simulate sequencing

Examples

  • Just read the input annotation, specified by the corresponding parameter REF_FILE_NAME in the parameter file test.par with this command
sim -p test.par
  • To read the input annotation and perform the expression simulation, try
sim -xp test.par
  • To continue the partially performed run with simulated library construction and sequencing, type
sim -lsp test.par
  • You can find a sample console output of a complete run here, the corresponding command would be
FluxSimulator-v1.2-j1.5/bin/sim.sh -p FluxSimulator-v1.2-j1.5/demo/testRun.par -xls

The Splice-Junction Extractor

The Splice-Junction Extractor retrieves the sequences of all possible splice juntions that can be derived from splice sites in the intron annotation. Output comes in form of multi-FASTA lines, each one containing 50nt exonic sequence on each side of an intron, respectively the lengths defined by -5flank and -3flank. To limit the donor/acceptor possibilities, an intron model is provided, per default introns between ~70nt and ~700,000nt with canonical GT/AG splice sites are considered as real introns. The descriptor of each FASTA entry has the format

> locusID _ 5'site _ 3'site _ *

with locusID describing the region of the splicing locus in a UCSC compatible string, 5'site and 3'site provide the coordinates of the up-, respectively downstream splice site, and a trailing * indicates that the intron shows evidence for splicing in the reference annotation.

Parameter Argument Modality Description
[-j|-sj|--junctions] String mandatory extract splice junctions (GTF file)
[-g|--genome] String mandatory set the path to the directory with genomic sequences (-sj)
[-5flank] String optional exonic flank 5' of intron (-sj)
[-3flank] String optional exonic flank 3' of intron (-sj)
[-imodel|--imodel] String optional specify the introm model (-sj)

Examples

  • Given an annotation myGenes.gtf on a directory with chromosomal sequences myBeast/*.fa, to extract 50nt upstream and downstream of all GT/AG pairs in each locus that are at least 70nt and maximally 700,000nt away from each other, try
sim -j myGenes.gtf -g myBeast
  • To adapt the flanking sequences to 30nt upstream and 70nt downstream
sim -j myGenes.gtf -g myBeast -5flank 30 -3flank 70
sim -j myGenes.gtf -g myBeast -imodel myBeastsIntrons.iml
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