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