tRNAscan-SE - detection of transfer RNA genes in genomic sequence

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

tRNAscan-SE 2.0.9+ds                                July 2021                                     TRNASCAN-SE(1)

       tRNAscan-SE 2.0.9 (July 2021) Copyright © 2020 Patricia Chan and Todd Lowe

              University of California Santa Cruz

       Freely distributed under the GNU General Public License (GPLv3)

              Scan a sequence file for tRNAs

       -- default: use Infernal & tRNA covariance models

              with eukaryotic sequences (use 'Search Mode Options' below to scan other types of sequences)

       Search Mode Options:

       -E     : search for eukaryotic tRNAs (default)

       -B     : search for bacterial tRNAs

       -A     : search for archaeal tRNAs

       -M <model>
              : search for mitochondrial tRNAs options: mammal, vert

       -O     : search for other organellar tRNAs

       -G     : use general tRNA model (cytoslic tRNAs from all 3 domains included)

       --mt <model>
              :  use  mito  tRNA  models  for  cytosolic/mito  detemination  (if  not  specified, only cytosolic
              isotype-specific model scan will be performed)

       -I     : search using Infernal default use with -E, -B, -A, or -G; optional for -O--max  : maximum sensitivity mode - search using Infernal without hmm filter (very slow)

       -L     : search using the legacy method (tRNAscan, EufindtRNA, and COVE) use with -E, -B, -A or -G-C--cove
              : search using COVE analysis only (legacy, extremely slow) default use with -O-H--breakdown
              : show breakdown of primary and secondary structure components to covariance model bit scores

       -D--nopseudo
              : disable pseudogene checking

       Output options:

       -o--output <file>
              : save final results in <file>

       -f--struct <file>
              : save tRNA secondary structures to <file>

       -s--isospecific <file>
              : save results using isotype-specific models in <file>

       -m--stats <file>
              : save statistics summary for run in <file> (speed, # tRNAs found in each part of search, etc)

       -b--bed <file>
              : save results in BED file format of <file>

       -j--gff <file>
              : save results in GFF3 file format of <file>

       -a--fasta <file>
              : save predicted tRNA sequences in FASTA file format of <file>

       -l--log <file>
              : save log of program progress in <file>

       --detail
              : display prediction outputs in detailed view

       --brief
              : brief output format (no column headers)

       -? #   : '#' in place of <file> chooses default name for output files

       -p--prefix <label>
              : use <label> prefix for all default output file names

       -d--progress
              : display program progress messages

       -q--quiet
              : quiet mode (credits & run option selections suppressed)

       -y--hitsrc
              : show origin of hits (Ts=tRNAscan 1.4, Eu=EufindtRNA, Bo=Both Ts and Eu, Inf=Infernal)

       Specify Alternate Cutoffs / Data Files:

       -X--score <score>
              : set cutoff score (in bits) for reporting tRNAs (default=20)

       -g--gencode <file>
              : use alternate genetic codes specified in <file> for determining tRNA type

       -z--pad <number>
              : use <number> nucleotides padding when passing first-pass tRNA bounds predictions to CM  analysis
              (default=8)

       --len <length>
              : set max length of tRNA intron+variable region for legacy search mode (default=116bp)

       Misc Options:

       -h--help
              : print this help message

       -c--conf <file>
              : tRNAscan-SE configuration file (default: tRNAscan-SE.conf)

       -Q--forceow
              : do not prompt user before overwriting pre-existing result files  (for batch processing)

       --match <EXPR>
              :  search  only  sequences  with  names matching <EXPR> string (<EXPR> may contain * or ? wildcard
              chars)

       --search <EXPR>
              : start search at sequence with name matching <EXPR> string and continue to end of input  sequence
              file(s)

       Special Advanced Options (for testing & special purposes)

       -U     : search for tRNAs with alternate models defined in configuration file

       -t--tscan
              : search using tRNAscan only (defaults to strict params)

       --tmode <mode>
              : explicitly set tRNAscan params, where <mode>=R or S (R=relaxed, S=strict tRNAscan v1.3 params)

       -v--verbose <file>
              : save verbose tRNAscan 1.3 output to <file>

       --nomerge
              : Keep redundant tRNAscan 1.3 hits (don't filter out multiple predictions per tRNA identification)

       -e--eufind
              :  search using Eukaryotic tRNA finder (EufindtRNA) only (defaults to Normal seach parameters when
              run alone, or to Relaxed search params when run with Cove)

       --emode <mode>
              : explicitly set EufindtRNA params, where <mode>=R, N, or S (relaxed, normal, or strict)

       --iscore <score>
              : manually set "intermediate" cutoff score for EufindtRNA

       -r--fsres <file>
              : save first-pass scan results from EufindtRNA, tRNAscan, or Infernal hmm  in  <file>  in  tabular
              results format

       --mid  : fast scan mode - search using Infernal with mid-level strictness of hmm filter

       -F--falsepos <file>
              :  save  first-pass  candidate  tRNAs  in  <file>  that  were  then found to be false positives by
              second-pass analysis

       --missed <file>
              : save all seqs that do NOT have at least one tRNA prediction in them (aka "missed" seqs)

       --thread <number>
              : number of threads used for running infernal (default is to use available threads)

       tRNAscan-SE - detection of transfer RNA genes in genomic sequence

tRNAscan-SE [-options] <FASTAfile(s)>