Man page - micro_razers(1)

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• rabema_evaluate(1)
• alf(1)
• mason_materializer(1)
• pair_align(1)
• gustaf(1)
• stellar(1)
• razers3(1)
• sak(1)
• yara_indexer(1)
• mason_frag_sequencing(1)
• micro_razers(1)
• rabema_prepare_sam(1)
• insegt(1)
• rabema_build_gold_standard(1)
• splazers(1)
• seqan_tcoffee(1)
• yara_mapper(1)
• tree_recon(1)
• mason_genome(1)
• mason_methylation(1)
• razers(1)
• snp_store(1)
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Manual

MICRO_RAZERS

NAME
SYNOPSIS
DESCRIPTION
REQUIRED ARGUMENTS
OPTIONS
Main Options::
Output Options::

---

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 .

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