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Bam2roi

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

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]

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.)

Best Friends (Incoming)

  • SamToBam (50 %) 
  • SortBam (50 %) 

Installation

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

KNIME 4.2

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

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Developers

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