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RoiFeatureProjection

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Compute the projection of a ROI file to regions from a BED or GFF file. The result is a ROI file where each interval from the BED/GFF/GTF file that overlapped with one input ROI file is a region of interest, with the coverage counts projected to the new region of interest.

Web Documentation for RoiFeatureProjection

Options

version-check
Turn this option off to disable version update notifications of the application.
quiet
Set verbosity to a minimum.
verbose
Enable verbose output.
very-verbose
Enable very verbose output.
mode
The mode in which to combine the ROI and BED/GFF file. See section Combination Modes below for details.
strand-specific
Enable strand-specific mode if set.
gff-type
The GFF/GTF record type (value of third column) to keep. Keep all if not set or input file type is not GFF/GTF.
gff-group-by
The GFF/GTF tag to use for grouping, e.g. "Parent", "transcript_id". No grouping if empty. When using the grouping feature, the --mode is automatically set to projection.

Input Ports

Icon
ROI file to read. [roi,roi.bgzf,roi.gz]
Icon
BED, GFF, or GTF file to read. [bed,bed.bgzf,bed.gz,gff,gff.bgzf,gff.gz,gff3,gff3.bgzf,gff3.gz,gtf,gtf.bgzf,gtf.gz]
Icon
Path to FASTA file with genome; optional. When given, this is used for computing the overall region's C+G content. [fasta,fa,opt.]

Output Ports

Icon
ROI file to write. [roi]

Views

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

Installation

To use this node in KNIME, install SeqAn from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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