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micro_razers - Online in the Cloud

Run micro_razers in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command micro_razers that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


micro_razers

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.

(c) Copyright 2009 by Anne-Katrin Emde.

-h, --help

Displays this help message.

--version

Display version information

Main Options::

-o, --output FILE

Change output filename. Default: <READS FILE>.result.

-rr, --recognition-rate NUM

set the percent recognition rate In range [80..100]. Default: 100.

-sL, --seed-length NUM

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 NUM

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 Format Options::

-of, --output-format NUM

Set output format. 0 = MicroRazerS format, 1 = SAM. In range [0..1].

-a, --alignment

dump the alignment for each match

-gn, --genome-naming NUM

Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In
range [0..1]. Default: 0.

-rn, --read-naming NUM

Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In
range [0..1]. Default: 0.

-so, --sort-order NUM

Select how matches are sorted. 0 = read number, 1 = genome position. In range
[0..1]. Default: 0.

-pf, --position-format NUM

Select begin/end position numbering (see Coordinate section below). 0 = gap space,
1 = position space. In range [0..1]. Default: 0.

VERSION

micro_razers version: 1.0.1 Last update Jul 2009

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