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 20090710Septembera2009 MICRORAZERS(1)