IconMicroRazers0 ×

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

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.

Web Documentation for MicroRazers

Options

version-check
Turn this option off to disable version update notifications of the application.
recognition-rate
set the percent recognition rate
seed-length
seed length
seed-error
allow for one error in the seed
forward
map reads only to forward strands.
reverse
map reads only to reverse strands.
match-N
'N' matches with all other characters
max-hits
output only NUM of the best hits
purge-ambiguous
purge reads with more than max-hits best matches
low-memory
decrease memory usage at the expense of runtime
verbose
verbose mode
vverbose
very verbose mode
alignment
dump the alignment for each match
genome-naming
Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1.
read-naming
Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1.
sort-order
Select how matches are sorted. 0 = read number, 1 = genome position.
position-format
Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space.

Input Ports

A reference genome file. [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]
Either one (single-end) or two (paired-end) read files. [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Output Ports

Change output filename. (use - to dump to stdout in razers format) Default: <READS FILE>.razers. [razers,sam,Inactive]

Views

MicroRazers Std Output
The text sent to standard out during the execution of MicroRazers.
MicroRazers Error Output
The text sent to standard error during the execution of MicroRazers. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: SeqAn from the following update site:

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