A.2.1 - Parameter File Format .PAR

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.

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, ...