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FastqcStatisticMerger

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

FastQC outputs statistics for each of its modules. The FastqcStatisticMerger can be used to merge the statistics into one file in order to post-process the data.

Options

Path to folder with FastQC Outputs
The node searches recursively all folders and sub-folders of the input directory for output files of a FastQC run.
Path to output folder
Set the path to the folder where the output files should be stored. The files will be named after the selected modules.
Modules to merge
Select by which modules the data should be merged. At least one module must be selected.
  • Basic Statistics
  • Per base sequence quality
  • Per sequence quality score
  • Per base sequence content
  • Per base GC content
  • Per sequence GC content
  • Per base N content
  • Sequence Length Distribution
  • Sequence Duplication Levels
  • Overrepresented sequences
  • Filter-Options Collector
  • Merge Status of all Modules - merges the status of all modules (pass, warn or fail are possible FastQC status values)
  • Merge ALL Modules - selects or de-selects all modules

Output Ports

Icon
Cell 0: Name of the module
Cell 1: Path to merged file
Icon
Cell 0: Path to FastQC output files which were merged

Views

No view implemented.

Best Friends (Outgoing)

Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

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Developers

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