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TranscriptionDetector [options] -sequence=file_name -expression=file_name ...

  Required parameters:
    -sequence=file_name    --- tab-delimited probe sequence file for all probes
                               (including negative control probes)
    -expression=file_name  --- tab-delimited expression file for all probes
                               (including negative control probes)
    -ncp_pvalue_file=name  --- list of negative control probe IDs used for
                               P-VALUE CALCULATION, one per line
    -ncp_seq_file=name     --- list of negative control probe IDs used for
                               SEQUENCE CORRECTION, one per line
                               (mandatory unless "noseq_correction" is set,
                                   usually the same as "ncp_pvalue_file")
    -output=file_name      --- name of output file

  Optional parameters:
    [-fdr_value=float]     --- FDR threshold (0.01)
    [-directory=string]    --- output directory (".", current directory)
    [-noseq_correction]    --- switch for omitting sequence correction
    [-exclude_ncp]         --- switch for excluding NCPs from output hit list
    [-verbose]             --- switch for outputting auxiliary files
    [-help]                --- print out this help message

    NB: o the parameters must follow the -parameter=value format, except for the
          four switches -noseq_correction, -exclude_ncp, verbose, and -help.
        o each -parameter can be abbreviated as long as non-ambiguity exists,
          e.g., -s=seq_file; -f=0.001 etc.
        o value in () are the default values, e.g., fdr_value is default to 0.01

    Run script "TRANSCRIPTIONDETECTOR_setup" for detailed installation instructions

  Usage:
    Suppose your are at $TRANSCRIPTIONDETECTOR/examples
    
    TranscriptionDetector -expr=log_EPNEPRO -s=probeVsId_EPNEPRO \
         -ncp_p=RO.idlist -ncp_s=RO.idlist -o=sample.out
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