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):
Key | Type | Default Value | Description |
---|---|---|---|
ANNOTATION_FILE | String | Path to the GTF reference annotation, either absolute or relative to the location of the parameter file | |
COVERAGE_FILE | String | Path to the file to which coverage profiles are stored; used only if COVERAGE_STATS is true | |
INSERT_FILE | String | Path to the file for output of inserts | |
KEEP_SORTED | String | Path to the directory where sorted file have to be stored in case of unsorted input files (ANNOTATION_FILE, MAPPING_FILE or both) | |
MAPPING_FILE | String | Path to the BED file containing the all the mappings. | |
PROFILE_FILE | String | Path to the file for outputting profiles | |
STATS_FILE | String | Path to the file to which the run characteristics are written | |
STDERR_FILE | String | Path to the file for log messages | |
STDOUT_FILE | String | Path to the file for default output | |
TMP_DIR | String | $TMP_DIR | Temporary directory, can also be specified by the environment variable $TMP_DIR. |
Key | Type | Default Value | Description |
---|---|---|---|
COVERAGE_STATS | Boolean | false | Flag to output coverage statistics |
STATS_FILE_APPEND | Boolean | false | Append to the stats file. This adds results from this run to an existing capacitor stats file. |
Key | Type | Default Value | Description |
---|---|---|---|
SORT_IN_RAM | Boolean | false | Sort reads in RAM memory, not on disk |
READ_DESCRIPTOR | String | default | Expression how to parse the read IDs, or one of the following shorthand names: ANTISENSE, STRAND_MATE, BARNA, MATE2_SENSE, MATE1_SENSE, MATE_STRAND_CSHL, SENSE, SIMULATOR, PAIRED, SIMPLE, CASAVA18 |
Key | Type | Default Value | Description |
---|---|---|---|
PCR_DISTRIBUTION | String | default | PCR distribution file, 'default' to use a distribution with 15 rounds and 20 bins, 'none' to disable amplification. |
PCR_PROBABILITY | Float | 0.1 | PCR duplication probability when GC filtering is disabled by setting GC_MEAN to NaN. |
GC_MEAN | Float | 0.5 | Mean value of a gaussian distribution that reflects GC bias amplification probability, set this to 'NaN' to disable GC biases. |
GC_SD | Float | 0.1 | Standard deviation of a gaussian distribution that reflects GC bias amplification probability, inactive if GC_MEAN is set to NaN. |
Key | Type | Default Value | Description |
---|---|---|---|
READ_NUMBER | Integer | 5,000,000 | Number of reads. |
READ_LENGTH | Integer | 36 | Length of the reads. |
PAIRED_END | Boolean | NO | Switch on/off paired-end reads. |
FASTA | Boolean | NO | 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. |
ERR_FILE | String | 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. | |
UNIQUE_IDS | Boolean | NO | Create unique read identifiers for paired reads. Information about the relative orientation is left out of the read id and encoded in the pairing information. All /1 reads are sense reads, all /2 reads are anti-sense reads. This option is useful if you want to identify paired reads based on the read ids. |