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).