IconInsegt0 ×

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

INSEGT is a tool to analyze alignments of RNA-Seq reads (single-end or paired-end) by using gene-annotations.

Input to INSEGT is a SAM file containing the alignments and a file containing the annotations of the reference genome, either in GFF or GTF format.

Web Documentation for Insegt

Options

version-check
Turn this option off to disable version update notifications of the application.
fusion-output
Output filename for fusion-output, which contains exon tuple of gene fusions (Advanced option, currently no output port for KNIME).
ntuple
ntuple
offset-interval
Offset to short alignment-intervals for search.
threshold-gaps
Threshold for allowed gaps in alignment (not introns).
threshold-count
Threshold for min. count of tuple for output.
threshold-rpkm
Threshold for min. RPKM of tuple for output.
max-tuple
Create only maxTuple (which are spanned by the whole read).
exact-ntuple
Create only Tuple of exact length n. By default all tuple up to the given length are computed (if -m is set, -e will be ignored).
unknown-orientation
Orientation of reads is unknown.

Input Ports

[sam]
[gff,gtf]

Output Ports

Output filename for read-output, which contains the mapped annotations followed by their parent annotation. [gff,Inactive]
Output filename for anno-output, which contains the annotations similar to the GFF input and additionally the counts of the mapped reads and the normalized expression levels in RPKM. [gff,Inactive]
Output filename for tuple-output, which contains exon tuples connected by reads or matepairs. [gff,Inactive]

Views

Insegt Std Output
The text sent to standard out during the execution of Insegt.
Insegt Error Output
The text sent to standard error during the execution of Insegt. (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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