micro_razers - Online in the Cloud

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

Use micro_razers online using onworks.net services