-tiac
tiac input file
Tiac input file (created by timegablast or tisearch)
Default value: n/a

-out
Output file prefix
Will be used to create output files with suffixes '.data', '.schema', '.report'
Default value: tiquery

-accs
File of accession numbers
Only processes the accession numbers specified in the file.
Default value: n/a

-acc
Accession number
Only processes the specified accession number. You can include as many -acc options as you wish.
Default value: n/a

-organism
Latin name for organism, e.g. Homo sapiens
Only looks at those ESTs from the given organism. You can define as many organisms as you wish.
Default value: n/a

-cache

Use a cache when connecting to the TissueInfo database. A cache can potentially speed up the querying of redundant tissue information.
Default value: n/a

-memory

Uses the flat file representation of the TissueInfo database and holds it in memory. Two files are required: ti_to and ti_seq. The pathnames of these files must be provided through the tissueinfo.path.ti_[to/seq] properties in crover.prp
Default value: n/a

-of

Turns on "Organism Fast" mode. Only activated in conjunction with -organism and -memory. Limits the amount of TissueInfo data held in memory. Data is only kept if it originates from the organisms specified through -organism. When -of is invoked, hits from organisms not specified by -organism are labelled as null in the result files (.report, .data)
Default value: n/a

-ser
Filename into which to put the cache

Default value: n/a

-purity
(double) amount of 'correctness' in sequence

Default value: 0.95

-isSpecificTo
Tissue
Determines whether the query sequence is expressed predominantly in the given tissue type.
Default value: n/a

-isSpecificToFile
File of tissues
Determines whether the query sequence is expressed predominantly in the tissues specified in the tissue file.
Default value: n/a

-isTissueSpecific

Determines whether the gene is tissue specific in its expression. If the gene is expressed in more than two tissues, it is defined as not being tissue specific.
Default value: n/a

-isExpressedIn
Tissue
Determines whether the query sequence is expressed in the given tissue type.
Default value: n/a

-isExpressedInFile
File of tissues
Determines whether the query sequence is expressed in the tissue types specified in the tissue file.
Default value: n/a

-mostExpressedIn

Gives the tissue type that the query sequence is predominantly expressed in.
Default value: n/a

-numPlant

Gives the number of hits for that query sequence that come from plant tissue.
Default value: n/a

-tissueSummary

Gives a list of all the tissues that the querysequence is shown to be expressed in
Default value: n/a

-report

Outputs a file with the output filename prefix, and a .report suffix which contains the raw dbEST organism and tissue library information for every EST match for each query sequence.
Default value: n/a

-nullCount

Reports how many of the EST matches for each query sequence do not have parseable organism and tissue library information in dbEST.
Default value: n/a

-numExpressedIn
Tissue
Gives the number of times that tissue is present in the matches found.
Default value: n/a