EUKHIGHCONFIDENCEFILTER(1)

Bestie, this is EUKHIGHCONFIDENCEFILTER(1) 💖 the manual for a tRNA-filtering tool, and it is giving main character energy 🦋

🌸 NAME 🌸

EukHighConfidenceFilter — basically, it's all about sniffing out transfer RNA genes in genomic sequence ✨

🎀 SYNOPSIS 🎀

EukQualityFilter [options]

💅 DESCRIPTION 💅

Okay so the options are where the magic happens 🔥 Here's the whole lineup:

• --result -i <file> — the tRNAscan-SE output file you feed in as input 📄
• --ss -s <file> — the tRNAscan-SE secondary structure file, also fed in as input 🧬
• --output -o <file path> — the directory where your output files get written 📂
• --prefix -p <name> — a prefix that gets slapped onto the output file name 🏷️
• --remove -r — removes the filtered tRNA hits 🗑️ (default: filtered tRNA hits are only tagged, not removed)
• --cmscore1 -c1 <num> — the domain-specific model score cutoff for secondary filtering 🎯 (default = 50; -1 if not used for filtering)
• --ssscore1 -m1 <num> — the secondary structure score cutoff for secondary filtering 🌷 (default = 10; -1 if not used for filtering)
• --isoscore1 -e1 <num> — the isotype-specific model score cutoff for secondary filtering 💜 (default = 70; -1 if not used for filtering)
• --isoscore2 -e2 <num> — the isotype-specific model starting score cutoff for tertiary filtering 🦄 (default = 70; -1 if not used for filtering)
• --isomaxscore2 -x <num> — the maximum isotype-specific model score cutoff for tertiary filtering 👑 (default = 95)
• --help -h — prints this help 🫧

🫶 AUTHOR 🫶

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

That's the whole page, bestie! 💖 This is EukHighConfidenceFilter 2.0.9+ds from July 2021, and I'm honestly obsessed 😭✨ Muah 💋