.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH MICRO_RAZERS "1" "June 2017" "micro_razers 2.3.1+dfsg-4" "User Commands"
.SH NAME
micro_razers \- Map small RNA reads possibly containing 3' adapter sequence
.PP
SYNOPSIS
.IP
micro_razers [OPTIONS] <GENOME FILE> <READS FILE>
.PP
DESCRIPTION
.IP
MicroRazerS uses a prefix\-based mapping strategy to map small RNA reads
possibly containing 3' adapter sequence.
.IP
Input to MicroRazerS is a reference genome file and a file with single\-end
reads. Use \- to read the reads from stdin.
.IP
(c) Copyright 2009 by Anne\-Katrin Emde.
.PP
REQUIRED ARGUMENTS
.IP
ARGUMENT 0 INPUT_FILE
.IP
A reference genome file. Valid filetypes are: .sam, .raw, .gbk,
\&.frn, .fq, .fna, .ffn, .fastq, .fasta, .faa, .fa, .embl, and .bam.
.IP
READS List of INPUT_FILE's
.IP
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.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.IP
Main Options::
.HP
\fB\-o\fR, \fB\-\-output\fR OUTPUT_FILE
.IP
Change output filename. (use \- to dump to stdout in razers format)
Default: <READS FILE>.razers. Valid filetypes are: .sam and .razers.
.HP
\fB\-rr\fR, \fB\-\-recognition\-rate\fR DOUBLE
.IP
set the percent recognition rate In range [80..100]. Default: 100.
.HP
\fB\-sL\fR, \fB\-\-seed\-length\fR INTEGER
.IP
seed length In range [10..inf]. Default: 16.
.HP
\fB\-sE\fR, \fB\-\-seed\-error\fR
.IP
allow for one error in the seed
.HP
\fB\-f\fR, \fB\-\-forward\fR
.IP
map reads only to forward strands.
.HP
\fB\-r\fR, \fB\-\-reverse\fR
.IP
map reads only to reverse strands.
.HP
\fB\-mN\fR, \fB\-\-match\-N\fR
.IP
\&'N' matches with all other characters
.HP
\fB\-m\fR, \fB\-\-max\-hits\fR INTEGER
.IP
output only NUM of the best hits In range [1..inf]. Default: 100.
.HP
\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
.IP
purge reads with more than max\-hits best matches
.HP
\fB\-lm\fR, \fB\-\-low\-memory\fR
.IP
decrease memory usage at the expense of runtime
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
verbose mode
.HP
\fB\-vv\fR, \fB\-\-vverbose\fR
.IP
very verbose mode
.IP
Output Options::
.HP
\fB\-a\fR, \fB\-\-alignment\fR
.IP
dump the alignment for each match
.HP
\fB\-gn\fR, \fB\-\-genome\-naming\fR INTEGER
.IP
Select how genomes are named. 0 = use Fasta id, 1 = enumerate
beginning with 1. In range [0..1]. Default: 0.
.HP
\fB\-rn\fR, \fB\-\-read\-naming\fR INTEGER
.IP
Select how reads are named. 0 = use Fasta id, 1 = enumerate
beginning with 1. In range [0..1]. Default: 0.
.HP
\fB\-so\fR, \fB\-\-sort\-order\fR INTEGER
.IP
Select how matches are sorted. 0 = read number, 1 = genome position.
In range [0..1]. Default: 0.
.HP
\fB\-pf\fR, \fB\-\-position\-format\fR INTEGER
.IP
Select begin/end position numbering (see Coordinate section below).
0 = gap space, 1 = position space. In range [0..1]. Default: 0.
.PP
VERSION
.IP
Last update:
micro_razers version: 1.0.9 [tarball]
SeqAn version: 2.3.1