MICRO_RAZERS(1)

✨ MICRO_RAZERS ✨

okay bestie, welcome to micro_razers(1) — the tool that maps small RNA reads that might be carrying a lil 3' adapter stowaway 💅

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🌸 NAME 🌸

micro_razers — map small RNA reads possibly containing 3' adapter sequence 🧬

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🎀 SYNOPSIS 🎀

micro_razers [OPTIONS] <GENOME FILE> <READS FILE>

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💖 DESCRIPTION 💖

MicroRazerS uses a prefix-based mapping strategy to map small RNA reads that possibly contain 3' adapter sequence. periodt. ✨

So the input is literally two things: a reference genome file and a file with single-end reads. Also — cute trick — if you pass - it reads the reads from stdin 🫶

(c) Copyright 2009 by Anne-Katrin Emde. 💜

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👑 REQUIRED ARGUMENTS 👑

ARGUMENT 0 INPUT_FILE

A reference genome file, no skips. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. 🦋

READS List of INPUT_FILE's

Either one (single-end) or two (paired-end) read files — your call, main character 💅 Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. 🍓

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✨ OPTIONS ✨

• -h, --help — shows you the help message 🫶
• --version — displays version information ⭐

🎀 Main Options:: 🎀

• -o, --output OUTPUT_FILE — change the output filename. (use - to dump to stdout in razers format) Default: <READS FILE>.razers. Valid filetypes are: .sam and .razers. 💖
• -rr, --recognition-rate DOUBLE — set the percent recognition rate. In range [80..100]. Default: 100. 🔥
• -sL, --seed-length INTEGER — seed length. In range [10..inf]. Default: 16. ✨
• -sE, --seed-error — allow for one error in the seed 👀
• -f, --forward — map reads only to forward strands 🌈
• -r, --reverse — map reads only to reverse strands 🔄
• -mN, --match-N — 'N' matches with all other characters 🤝
• -m, --max-hits INTEGER — output only NUM of the best hits. In range [1..inf]. Default: 100. 💅
• -pa, --purge-ambiguous — purge reads with more than max-hits best matches 🧹
• -lm, --low-memory — decrease memory usage at the expense of runtime 😭 (trade-offs, babe)
• -v, --verbose — verbose mode 🗣️
• -vv, --vverbose — very verbose mode 💀 (yes, very)

🦋 Output Options:: 🦋

• -a, --alignment — dump the alignment for each match 📋
• -gn, --genome-naming INTEGER — Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0. 👑
• -rn, --read-naming INTEGER — Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0. 🌸
• -so, --sort-order INTEGER — Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0. ⭐
• -pf, --position-format INTEGER — Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: 0. 🎀

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no cap, that's the whole page — every flag, every range, every default, all of it 💖

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and that's a wrap bestie!! this is micro_razers version 1.0.15 [tarball] — go map some reads and slay 💅✨🫶