NAME

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

SYNOPSIS

       tRNAscan-SE [-options] <FASTA file(s)>

DESCRIPTION

       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)

AUTHOR

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