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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

KeyTypeDefault ValueDescription
ANNOTATION_FILEString 

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

COVERAGE_FILEString 

Path to the file to which coverage profiles are stored; used only if COVERAGE_STATS is true

INSERT_FILEString 

Path to the file for output of inserts

KEEP_SORTEDString 

Path to the directory where sorted file have to be stored in case of unsorted input files (ANNOTATION_FILE, MAPPING_FILE or both)

MAPPING_FILEString 

Path to the BED file containing the all the mappings.

PROFILE_FILEString Path to the file for outputting profiles
STATS_FILEString Path to the file to which the run characteristics are written
STDERR_FILEString Path to the file for log messages
STDOUT_FILEString Path to the file for default output
TMP_DIRString$TMP_DIRTemporary directory, can also be specified by the environment variable $TMP_DIR.

Output

KeyTypeDefault ValueDescription
COVERAGE_STATSBooleanfalseFlag to output coverage statistics
STATS_FILE_APPENDBooleanfalse

Append to the stats file. This adds results from this run to an existing capacitor stats file.

 

Input

KeyTypeDefault ValueDescription
SORT_IN_RAMBooleanfalseSort reads in RAM memory, not on disk
READ_DESCRIPTORStringdefault

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

Amplification

KeyTypeDefault ValueDescription
PCR_DISTRIBUTIONStringdefault

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

PCR_PROBABILITYFloat0.1PCR duplication probability when GC filtering is disabled by setting GC_MEAN to NaN.
GC_MEANFloat0.5

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

GC_SDFloat0.1

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

Sequencing

KeyTypeDefault ValueDescription
READ_NUMBERInteger5,000,000Number of reads.
READ_LENGTHInteger36Length of the reads.
PAIRED_ENDBooleanNOSwitch on/off paired-end reads.
FASTABooleanNO

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_FILEString 

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_IDSBooleanNOCreate 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.
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