The PAR format in the Flux Simulator is used to administrate all parameters of a run. It is a simple format containing key value pairs (one per line) with the following parameter names (i.e., keys):
File Locations
| Key | Value | Description |
|---|---|---|
| REF_FILE_NAME | String | Path to the GTF 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; the default profile uses the name of the parameter file with the extension .pro. |
| LIB_FILE_NAME | String | 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. |
| SEQ_FILE_NAME | String | 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. |
| GEN_DIR | String | 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. |
Expression
| Key | Value | Description |
|---|---|---|
| Key | Value | Description |
|---|---|---|
| File locations | ||
| 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. |
| Expression | ||
| 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). |
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