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Path

to the GTF reference annotation, either absolute or relative to the location of the parameter file

Path

to the profile of the run, either absolute or relative to the location of the parameter file; the default profile uses the name of the parameter file with the extension .pro.

Path

to the library file of the run, either absolute or relative to the location of the parameter file; the default profile uses the name of the parameter file

with the extension .lib.

Path

to the

sequencing file

of the

run, either absolute or relative to the location of the parameter file; the default profile uses the name of the parameter file with the extension .bed.

Path to the directory with the genomic sequences

, i.e., one fasta file per chromosome/scaffold/contig with a file name corresponding to the identifiers of the first column in the GTF annotation.

TSS_MEAN

POLYA_SCALE

POLYA_SHAPE

RNA*

*DNA in Simulator

v1.2 and earlier

Substrate of fragmentation, determines the order of fragmentation and reverse transcription (RT):

     for substrate DNA, fragmentation is carried out after RT,

     substrate RNA triggers fragmentation before RT.

Fragmentation method employed:

     * [EZ] Fragmentation by enzymatic digestion

     * [NB] Fragmentation by nebulization

     * [UR] Uniformal random fragmentation

Sequence motif caused by selective restriction with an enzyme, choose pre-defined NlaIII, DpnII, or a file with a custom position weight matrix.

Threshold on the fraction of the molecule population; if less molecules break per time unit, convergence to steady state is assumed.

Average expected framgent size after fragmentations, i.e., number of breaks per unit length (exhautiveness of fragmentation);

NaN optimizes the fragmentation process w.r.t. the size filtering

Geometry of molecules in the UR process:

     * NaN= depends logarithmically on molecule length,

     * 1= always linear,

     * 2= always surface-diameter,

     * 3= volume-diameter, ...

Primers used for first strand synthesis:

     * [RH] for random hexamers or

     * [PDT] for poly-dT primers

Minimum fragment length observed after reverse transcription of full-length transcripts.

Maximum fragment length observed after reverse transcription of full-length transcripts.

Size distribution of fragments after filtering, either specified by the fully qualified path of a file with an empirical distribution where each line represents the length of a read (no ordering required), or attributes of a gaussian distribution (mean and standard deviation) in the form , for example . If no size distribution is provided, an empirical Illumina fragment size distribution is employed.

PCR distribution file, 'default' to use a distribution with 15 rounds and 20 bins, 'none' to disable amplification.

Mean value of a gaussian distribution that reflects GC bias amplification probability, set this to 'NaN' to disable GC biases.

Standard deviation of a gaussian distribution that reflects GC bias amplification probability, inactive if GC_MEAN is set to NaN.

Creates .fasta/.fastq output. Requires the genome sequences in a folder specified by GEN_DIR. If a quality model is provided by parameter ERR_FILE, a .fastq file is produced. Otherwise read sequences are given as .fasta.

Path to the file with the error model. With the values '35' or '76', default error models are provided for the corresponding read lengths, otherwise the path to a custom error model file is expected.