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RoiFeatureProjection

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

: ROI file to read. [roi,roi.bgzf,roi.gz]
: 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]
: 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

: ROI file to write. [roi]

Popular Predecessors

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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.)

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Developers

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Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Plugin version: 2.4.1.202004061533

On NodePit since: 2022-12-06

Last update: 2024-12-16

KNIME versions: From v3.6 to v4.7

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