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.