Miscellaneous Options

-h

: print full list of available program options

Prints this list of program options, each with a brief, one-line description.

-Q

: do not prompt user before overwriting pre-existing files

By default, if an output result file to be written to already exists, the user is prompted whether the file should be over-written or appended to. Using this options forces overwriting of pre-existing files without an interactive prompt. This option may be handy for batch-processing and running tRNAscan-SE in the background.

-n expr

: search only sequences with names matching expr string

This option allows analysis of selected sequences in a sequence file containing multiple sequences. Only those sequences with names (first non-white space word after ``>'' symbol on FASTA name/description line) matching expr are analyzed. expr may contain * or ? wildcard characters, but the user should enclose such expressions in single quotes (for example: -n 'HU?alpha*') to prevent the shell from attempting to expand wildcards into file name matches.

-s expr

: start search at sequence with name matching expr string and continue to end of input sequence file(s)

This option directs the program to analyze the first sequence with a name matching expr, and every sequence thereafter. This may be useful for re-starting crashed/aborted runs at the point where the previous run stopped. (if same names for output file(s) are used, program will ask if files should be over-written or appended to --- choose append and run will successfully be restarted where it left off).