Bam2roi

Calculated consecutive regions of coverage from alignment file IN.bam and write regions of interst to file OUT.roi. Counting is performed over the entire region (including intron and N-regions) based on the CIGAR string of the alignment record.

Web Documentation for Bam2roi

Options

version-check
Turn this option off to disable version update notifications of the application.
verbose
Verbose mode.
very-verbose
Very verbose mode.
strand-specific
Calculate strand-specific ROIs (see section Strand Specificness below.
ignore-pairing
Ignore paired information. Also see Section ROI Creation Details.
link-over-skipped
Link over skipped bases in the read alignment.

Input Ports

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SAM/BAM formatted file. Must be sorted by coordinate. [bam,sam,sam.bgzf,sam.gz]

Output Ports

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Output file with regions of interest. [roi,roi.bgzf,roi.gz]

Popular Predecessors

  • SamToBam50 %
  • SortBam50 %

Popular Successors

  • No recommendations found

Views

Bam2roi Std Output
The text sent to standard out during the execution of Bam2roi.
Bam2roi Error Output
The text sent to standard error during the execution of Bam2roi. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Links

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: 2026-01-01
KNIME versions: From v3.6 to v4.7

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