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Bisar

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

This program reads three-letter mappings of bisulfite reads and computes local pairwise four-letter realignments using an advanced statistical alignment model.

Web Documentation for Bisar

Options

version-check
Turn this option off to disable version update notifications of the application.
max3-error
Max. error rate in 3-letter alphabet.
max4-error
Max. error rate in 4-letter alphabet.
min-mapq
Min required mapping quality.
ns-subst-errors
Use empirical substitution error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Dohm et al. 2008).
ns-ins-errors
Use empirical insertion error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Minoche et al. 2011).
ns-del-errors
Use empirical deletion error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Minoche et al. 2011).
del-error-rate
Deletion error rate.
gap-open-score
Gap open score (original, must be proportional to mismatch scores).
gap-extend-score
Gap extend score.
bs-conversion-rate
Bisulfite conversion rate.
global-meth-rate
Global methylation rate.
seq-identity
Sequence identity used for substitution matrix.
ref-n
Rate of Ns in reference sequence.
quiet
Set verbosity to a minimum.
verbose
Enable verbose output.
very-verbose
Enable very verbose output.

Input Ports

SAM input file containing three-letter read alignments (must be sorted by query names). [bam,sam,sam.bgzf,sam.gz]
A reference genome file. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
Either one (single-end) or two (paired-end) read files. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]

Output Ports

Mapping output file. [bam,sam,sam.bgzf,sam.gz]

Views

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

Workflows

Update Site

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

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