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