micro_razers - Map small RNA reads possibly containing 3' adapter
sequence
micro_razers [OPTIONS] <GENOME FILE>
<READS FILE>
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.
- 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.
- -h, --help
- Display the help message.
- --version
- Display version information.
- -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