MICRORAZERS(1)

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).