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MICRO_RAZERS(1) MICRO_RAZERS(1)

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
-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.
micro_razers 1.0.10 [tarball]