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The PAR format in the Flux Capacitor 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_RAMBooleantrueSort reads in RAM memory, not on disk
READ_DESCRIPTORString{ID}

Expression how to parse the read IDs, or one of the following shorthand names:

NR_READS_MAPPEDInt-1

The number of reads mapped

ANNOTATION_MAPPINGString
SINGLE

Information from the read descriptor that will be used for annotation mapping:

Task

KeyTypeDefault ValueDescription
NO_DECOMPOSEBooleanfalse

Avoid running deconvolution step on the dataset

COUNT_ELEMENTSList[]

Count elements specified in the list:

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