---
name: "micro_razers"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/micro_razers"
---

# micro\_razers(1)

Map small RNA reads possibly containing 3' adapter sequence

## NAME

micro\_razers - Map small RNA reads possibly containing 3' adapter sequence

## SYNOPSIS

**micro\_razers** \[*OPTIONS*\] \<*GENOME FILE*\> \<*READS FILE*\>

## DESCRIPTION

MicroRazerS uses a prefix-based mapping strategy to map small RNA reads possibly containing 3' adapter sequence.

Input to MicroRazerS is a reference genome file and a file with single-end reads. Use - to read the reads from stdin.

(c) Copyright 2009 by Anne-Katrin Emde.

## REQUIRED ARGUMENTS

- **ARGUMENT 0** *INPUT\_FILE*

  A reference genome file. Valid filetypes are: *.sam\[.\*\]*, *.raw\[.\*\]*, *.gbk\[.\*\]*, *.frn\[.\*\]*, *.fq\[.\*\]*, *.fna\[.\*\]*, *.ffn\[.\*\]*, *.fastq\[.\*\]*, *.fasta\[.\*\]*, *.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. Valid filetypes are: *.sam\[.\*\]*, *.raw\[.\*\]*, *.gbk\[.\*\]*, *.frn\[.\*\]*, *.fq\[.\*\]*, *.fna\[.\*\]*, *.ffn\[.\*\]*, *.fastq\[.\*\]*, *.fasta\[.\*\]*, *.faa\[.\*\]*, *.fa\[.\*\]*, *.embl\[.\*\]*, and *.bam*, where \* is any of the following extensions: *gz*, *bz2*, and *bgzf* for transparent (de)compression.

## OPTIONS

- **-h**, **--help**

  Display the help message.

- **--version**

  Display version information.

### Main Options::

- **-o**, **--output** *OUTPUT\_FILE*

  Change 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

- **-v**, **--verbose**

  verbose mode

- **-vv**, **--vverbose**

  very verbose mode

### 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*.