TRNASCAN-SE(1)

💖 tRNAscan-SE — the manual, but make it cute 💖

okay bestie, welcome to TRNASCAN-SE(1), a User Commands moment. this is the tRNA gene finder and she is iconic. let's get into it. 🧬✨

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🌸 NAME 🌸

tRNAscan-SE — detection of transfer RNA genes in genomic sequence. literally what she says on the tin, no cap. 🦋

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✨ SYNOPSIS ✨

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

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💅 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). slay, open source rights. 👑

Scan a sequence file for tRNAs — that's the whole vibe.

-- default: use Infernal & tRNA covariance models, with eukaryotic sequences. (use 'Search Mode Options' below to scan other types of sequences, bestie, don't just assume everyone's a eukaryote 💀)

🔍 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 are: 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. > heads up bestie: very slow. like, go-make-a-snack 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) 🔥

these ones are for the girlies doing science experiments, okay? handle with care. 🙈

• -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)

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👑 AUTHOR 👑

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

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and that's the whole page, bestie!! 🎀✨

tRNAscan-SE 2.0.9+ds — July 2021 — you're welcome, mwah. 💅🫶🌸