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.

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Main Options::

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

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

seed length In range [10..inf]. Default: 16.

allow for one error in the seed

map reads only to forward strands.

map reads only to reverse strands.

'N' matches with all other characters

output only NUM of the best hits In range [1..inf]. Default: 100.

purge reads with more than max-hits best matches

decrease memory usage at the expense of runtime

verbose mode

very verbose mode

Output Format Options::

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

dump the alignment for each match

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

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

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

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