NAME

       MicroRazerS - Rapid Alignment of Small RNA Reads

SYNOPSIS

       micro_razers [OPTION]... <GENOME FILE> <READS FILE>

DESCRIPTION

       MicroRazerS - Rapid Alignment of Small RNA Reads

   Main Options:
       -o,  --output FILE
              change output filename (default <READS FILE>.result)

       -sL, --seed-length NUM
              seed length (default 16)

       -sE, --seed-error
              allow for one error in the seed (default off)

       -rr, --recognition-rate
              set lower bound of sensitivity level for one-error matches (default 100)

       -f,  --forward
              only compute forward matches

       -r,  --reverse
              only compute reverse complement matches

       -mN, --match-N
              'N' matches with all other characters

       -m,  --max-hits NUM
              output only NUM of the best hits (default 100)

       -pa, --purge-ambiguous
              purge reads with more than max-hits best matches

       -lm, --low-memory
              may decrease memory usage at the expense of runtime

       -v,  --verbose
              verbose mode

       -vv, --vverbose
              very verbose mode

       -V,  --version
              print version number

       -h,  --help
              print this help

   Output Format Options:
       -a,  --alignment
              dump the alignment for each match

       -gn, --genome-naming NUM
              select  how  genomes  are  named 0 = use Fasta id (default) 1 = enumerate beginning
              with 1

       -rn, --read-naming NUM
              select how reads are named 0 = use Fasta id (default) 1 = enumerate beginning  with
              1 2 = use the read sequence (only for short reads!)

       -so, --sort-order NUM
              select  how matches are sorted 0 = 1. read number, 2. genome position (default) 1 =
              1. genome position, 2. read number

       -pf, --position-format
              0 = gap space (default) 1 = position space

AUTHOR

       MicroRazerSwas written by Anne-Katrin Emde.

       This  manual  page  was  generated  using  html2man  and  polished  by  Soeren  Sonnenburg
       <sonne@debian.org>, for the Debian project (but may be used by others).

MicroRazerS version 0.1 20090710 (prereleaSeptember 2009                           MICRORAZERS(1)