micro_razers - Map small RNA reads possibly containing 3' adapter sequence

       MicroRazerS  uses  a  prefix-based mapping strategy to map small RNA reads possibly containing 3' adapter
       sequence.

       Input to MicroRazerS is a reference genome file and a file with single-end reads. Use - to read the reads
       from stdin.

       (c) Copyright 2009 by Anne-Katrin Emde.

       micro_razers - Map small RNA reads possibly containing 3' adapter sequence

-h, --help
              Display the help message.

       --version
              Display version information.

   MainOptions::-o, --outputOUTPUT_FILE
              Change  output  filename. (use - to dump to stdout in razers format) Default: <READSFILE>.razers.
              Valid filetypes are: .sam and .razers.

       -rr, --recognition-rateDOUBLE
              set the percent recognition rate In range [80..100]. Default: 100.

       -sL, --seed-lengthINTEGER
              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-hitsINTEGER
              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

   OutputOptions::-a, --alignment
              dump the alignment for each match

       -gn, --genome-namingINTEGER
              Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In  range  [0..1].
              Default: 0.

       -rn, --read-namingINTEGER
              Select  how  reads  are  named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1].
              Default: 0.

       -so, --sort-orderINTEGER
              Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0.

       -pf, --position-formatINTEGER
              Select begin/end position numbering (see Coordinate section below). 0 = gap space,  1  =  position
              space. In range [0..1]. Default: 0.

micro_razers 1.0.11 [tarball]                                                                    MICRO_RAZERS(1)

ARGUMENT0INPUT_FILE
              A reference genome file. Valid filetypes are: .sam[.*],  .raw[.*],  .gbk[.*],  .frn[.*],  .fq[.*],
              .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any
              of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

       READS List of INPUT_FILE's
              Either  one  (single-end) or two (paired-end) read files. Valid filetypes are: .sam[.*], .raw[.*],
              .gbk[.*], .frn[.*],  .fq[.*],  .fna[.*],  .ffn[.*],  .fastq[.*],  .fasta[.*],  .faa[.*],  .fa[.*],
              .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent
              (de)compression.

micro_razers [OPTIONS] <GENOMEFILE> <READSFILE>