PAR format

The format of the PAR (Simulation Parameters) files used by the FLUX SIMULATOR to administrate all parameters of a run. It is a tab-separated 2-column list of key value pairs and comprises the parameters:

key values description
REF_FILE_NAME String path to the reference annotation, either absolute or relative to the location of the parameter file
PRO_FILE_NAME String path to the profile of the run, either absolute or relative to the location of the parameter file
LIB_FILE_NAME [String] path to the library file, either absolute or relative to the location of the parameter file
BED_FILE_NAME SEQ_FILE_NAME String path to the bed file with the genomic annotation of the simulated sequencing reads, either absolute or relative to the location of the parameter file
GEN_DIR String path to the directory with the genomic sequences of chromosomes or scaffolds used in the reference annotation.
NB_MOLECULES [Integer] Number of initial RNA molecules in the simulation
LOAD_CODING [YES|NO] Flag to load coding transcripts from the reference annotation.
LOAD_NONCODING [YES|NO] Flag to load the non-coding transcripts, i.e., transcripts without CDS features, from the reference annotation
EXPRESSION_K Float Power law parameter $k$ of the expression simulation, should be <0.
EXPRESSION_X0 Integer Number of molecules for the highest expressed transcript, depends on NB_MOLECULES
EXPRESSION_X1 Float Parameter determing the exponential decay in the expression simulation
RT_PRIMER [RANDOM|POLY-DT] Flag to switch between random priming and poly-dT priming for the first strand synthesis of the reverse transcription
RT_MIN Integer Minimum length (in [nt]) of the expected reversely transcribed cDNA molecules
RT_MAX Integer Maximum length (in [nt]) of the expected reverse transcription products
FRAGMENTATION [YES|NO] Optional: flag that determines whether a fragmentation step is carried out
FRAG_B4_RT [YES|NO] flag to schedule the fragmentation before (YES), or after (NO) the reverse transcription. Note for fragmentations carried out before reverse transcription, exclusively random priming strategies are reasonable.
FRAG_MODE [PHYSICAL|CHEMICAL] flag to switch between fragmentation according to physical or chemical attributes.
FRAG_LAMBDA Integer Upper boundary of fragment lengths (in [nt]) that are not expected to be fragmented by the applied technique
FILTERING [YES|NO] Flag to indicate whether a length filtering step is carried out on the cDNA library.
FILT_MIN Integer Minimum length that is retained during filtering.
FILT_MAX Integer Maximum length that is retained during filtering.
READ_NUMBER Integer Number of reads that are intented to produce. Note: this number is an upper boundary and gets adapted to the actual size of the intermediary generated library.
READ_LENGTH Integer Length of the generated reads, depends on filtering settings.
PAIRED_END [YES|NO] Flag to indicate whether read pairs are produced.
FASTQ [YES|NO] Flag that indicates whether additionally the read sequences and qualities are output. Depends on GENOME_DIR and ERR_FNAME.
QTHOLD Integer Quality value below which base-calls are considered problematic.
TMP_DIR String Path to folder for temporary files, if different from system standard (commonly /tmp on Unix clones).

Add a New Comment
Unless otherwise stated, the content of this page is licensed under Creative Commons Attribution-ShareAlike 3.0 License