.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.1. .TH MICRO_RAZERS "1" "September 2014" "micro_razers 1.4.1+dfsg" "User Commands" .SH NAME micro_razers .PP SYNOPSIS .IP micro_razers [OPTIONS] .PP DESCRIPTION .IP MicroRazerS uses a prefix\-based mapping strategy to map small RNA reads possibly containing 3' adapter sequence. .IP (c) Copyright 2009 by Anne\-Katrin Emde. .HP \fB\-h\fR, \fB\-\-help\fR .IP Displays this help message. .HP \fB\-\-version\fR .IP Display version information .IP Main Options:: .HP \fB\-o\fR, \fB\-\-output\fR FILE .IP Change output filename. Default: .result. .HP \fB\-rr\fR, \fB\-\-recognition\-rate\fR NUM .IP set the percent recognition rate In range [80..100]. Default: 100. .HP \fB\-sL\fR, \fB\-\-seed\-length\fR NUM .IP seed length In range [10..inf]. Default: 16. .HP \fB\-sE\fR, \fB\-\-seed\-error\fR .IP allow for one error in the seed .HP \fB\-f\fR, \fB\-\-forward\fR .IP map reads only to forward strands. .HP \fB\-r\fR, \fB\-\-reverse\fR .IP map reads only to reverse strands. .HP \fB\-mN\fR, \fB\-\-match\-N\fR .IP \&'N' matches with all other characters .HP \fB\-m\fR, \fB\-\-max\-hits\fR NUM .IP output only NUM of the best hits In range [1..inf]. Default: 100. .HP \fB\-pa\fR, \fB\-\-purge\-ambiguous\fR .IP purge reads with more than max\-hits best matches .HP \fB\-lm\fR, \fB\-\-low\-memory\fR .IP decrease memory usage at the expense of runtime .HP \fB\-v\fR, \fB\-\-verbose\fR .IP verbose mode .HP \fB\-vv\fR, \fB\-\-vverbose\fR .IP very verbose mode .IP Output Format Options:: .HP \fB\-of\fR, \fB\-\-output\-format\fR NUM .IP Set output format. 0 = MicroRazerS format, 1 = SAM. In range [0..1]. .HP \fB\-a\fR, \fB\-\-alignment\fR .IP dump the alignment for each match .HP \fB\-gn\fR, \fB\-\-genome\-naming\fR NUM .IP Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0. .HP \fB\-rn\fR, \fB\-\-read\-naming\fR NUM .IP Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0. .HP \fB\-so\fR, \fB\-\-sort\-order\fR NUM .IP Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0. .HP \fB\-pf\fR, \fB\-\-position\-format\fR NUM .IP Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: 0. .PP VERSION .IP micro_razers version: 1.0.1 Last update Jul 2009