NAME

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

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.

       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.

REQUIRED ARGUMENTS

       ARGUMENT 0 INPUT_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.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Main Options::
       -o, --output OUTPUT_FILE
              Change  output filename. (use - to dump to stdout in razers format) Default: <READS
              FILE>.razers. Valid filetypes are: .sam and .razers.

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

       -sL, --seed-length INTEGER
              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 INTEGER
              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 Options::
       -a, --alignment
              dump the alignment for each match

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

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

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

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