2 - Getting Started

The Flux Simulator is written in 100% pure Java, therefore no platform-specific compiling of the bytecode is required. A Java Virtual Machine with level 1.6 or higher has to be installed on the system, however, it is recommended to update to the newest Java binaries provided by Oracle for the corresponding platform (i.e., Linux, Solaris, or Windows); Mac OSX users are encouraged to use the automatic software update functionality to obtain the newest virtual machine from Apple.

Besides of a java virtual machine, the Flux Simulator provides a wrapper script to launch the program from predominant shell interpreters of major platforms.

Random Access Memory (RAM) consumption of the Flux Simulator increases drastically with the simulation of sequence-dependent biases; an RNA-Seq experiment involving a typical mammalian transcriptome, for instance, can be simulated in substantially less than 1Gb of RAM when disregarding sequence specific biases. When sequence motifs are provided, however, the memory requirements increase to >3Gb of memory. Note that RAM requirements scale with the number of different transcripts that are simulated, regardless of how many expressed RNA molecules, fragments or reads are obtained from these in the end. Memory for a simulation run can be assigned by setting the environment variable FLUX_MEM:

In contrast to RAM, the requirements of disk space increase with the number of molecules (fragments and reads, respectively) that are simulated. The BED format used for storing the genomic location of every sequenced read: e.g., the ~300 million reads sequenced in the human experiment produce a .BED file of ~30 Gb, which corresponds to about 10 million reads that can be stored in 1 Gb. Sufficient disk resources are to be provided within the temporary directory and in the output directory.