.TH MICRO_RAZERS 1 "" "micro_razers 1.0.10 [tarball]" ""
.SH NAME
micro_razers \- Map small RNA reads possibly containing 3' adapter sequence
.SH SYNOPSIS
\fBmicro_razers\fP [\fIOPTIONS\fP] <\fIGENOME FILE\fP> <\fIREADS FILE\fP>
.SH DESCRIPTION
MicroRazerS uses a prefix-based mapping strategy to map small RNA reads possibly containing 3' adapter sequence. 
.sp
Input to MicroRazerS is a reference genome file and a file with single-end reads. Use - to read the reads from stdin.
.sp
(c) Copyright 2009 by Anne-Katrin Emde.
.SH REQUIRED ARGUMENTS
.TP
\fBARGUMENT 0\fP \fIINPUT_FILE\fP
A reference genome file. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fBREADS\fP List of \fIINPUT_FILE\fP's
Either one (single-end) or two (paired-end) read files. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Main Options::
.TP
\fB-o\fP, \fB--output\fP \fIOUTPUT_FILE\fP
Change output filename. (use - to dump to stdout in razers format) Default: <\fIREADS FILE\fP>.razers. Valid filetypes are: \fI.sam\fP and \fI.razers\fP.
.TP
\fB-rr\fP, \fB--recognition-rate\fP \fIDOUBLE\fP
set the percent recognition rate In range [80..100]. Default: \fI100\fP.
.TP
\fB-sL\fP, \fB--seed-length\fP \fIINTEGER\fP
seed length In range [10..inf]. Default: \fI16\fP.
.TP
\fB-sE\fP, \fB--seed-error\fP
allow for one error in the seed
.TP
\fB-f\fP, \fB--forward\fP
map reads only to forward strands.
.TP
\fB-r\fP, \fB--reverse\fP
map reads only to reverse strands.
.TP
\fB-mN\fP, \fB--match-N\fP
'N' matches with all other characters
.TP
\fB-m\fP, \fB--max-hits\fP \fIINTEGER\fP
output only NUM of the best hits In range [1..inf]. Default: \fI100\fP.
.TP
\fB-pa\fP, \fB--purge-ambiguous\fP
purge reads with more than max-hits best matches
.TP
\fB-lm\fP, \fB--low-memory\fP
decrease memory usage at the expense of runtime
.TP
\fB-v\fP, \fB--verbose\fP
verbose mode
.TP
\fB-vv\fP, \fB--vverbose\fP
very verbose mode
.SS Output Options::
.TP
\fB-a\fP, \fB--alignment\fP
dump the alignment for each match
.TP
\fB-gn\fP, \fB--genome-naming\fP \fIINTEGER\fP
Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: \fI0\fP.
.TP
\fB-rn\fP, \fB--read-naming\fP \fIINTEGER\fP
Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: \fI0\fP.
.TP
\fB-so\fP, \fB--sort-order\fP \fIINTEGER\fP
Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: \fI0\fP.
.TP
\fB-pf\fP, \fB--position-format\fP \fIINTEGER\fP
Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: \fI0\fP.