micro_razers1
Map small rna reads possibly containing 3' adapter sequence
Usage
micro_razers [OPTIONS]
<GENOME
FILE>
<READS
FILE>
Overview
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.
History
- Debian 13 (Trixie) to Debian 10 (Buster): the text shown here
- Debian 9 (Stretch)
- Debian 8 (Jessie)
- Debian 7 (Wheezy) to Debian 6.0 (Squeeze)
--alignment since Debian 10 (Buster);
--forward since Debian 10 (Buster);
--genome-naming since Debian 10 (Buster);
--help since Debian 10 (Buster);
--low-memory since Debian 10 (Buster);
--match-N since Debian 10 (Buster);
--max-hits since Debian 10 (Buster);
--output since Debian 10 (Buster);
--position-format since Debian 10 (Buster);
--purge-ambiguous since Debian 10 (Buster);
--read-naming since Debian 10 (Buster);
--recognition-rate since Debian 10 (Buster);
--reverse since Debian 10 (Buster);
--seed-error since Debian 10 (Buster);
--seed-length since Debian 10 (Buster);
--sort-order since Debian 10 (Buster);
--verbose since Debian 10 (Buster);
--version since Debian 10 (Buster);
--vverbose since Debian 10 (Buster);
-a since Debian 10 (Buster);
-f since Debian 10 (Buster);
-gn since Debian 10 (Buster);
-h since Debian 10 (Buster);
-lm since Debian 10 (Buster);
-m since Debian 10 (Buster);
-mN since Debian 10 (Buster);
-o since Debian 10 (Buster);
-pa since Debian 10 (Buster);
-pf since Debian 10 (Buster);
-r since Debian 10 (Buster);
-rn since Debian 10 (Buster);
-rr since Debian 10 (Buster);
-sE since Debian 10 (Buster);
-sL since Debian 10 (Buster);
-so since Debian 10 (Buster);
-v since Debian 10 (Buster);
-vv since Debian 10 (Buster).
-V until Debian 7 (Wheezy).