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FQCWriter

NGS related nodes for KNIME Workbench version 0.2.200.qualifier by Bernd Jagla, Institute Pasteur

Writes files such as the fastqc_data.txt file. Sections are stored in cells.

In general the file format consists of the following parts:

  1. comment lines (that can include the version of the tool that created the file)
    starts with "##" and is one line long
  2. Sections that can be regarded as individual tables starts with ">>" and ends with ">>END_MODULE" the first lines contains the name of the table, and an optional tab character followed by addition information (e.g. pass/fail)
  3. within a section the column header are identified by a line that starts with "#". Each column header is separated by a tab character
  4. Any other line within the Section follows the structure defined by the column header line. Values are tab separated
Example:
##FastQC	0.10.1
>>Basic Statistics	pass
#Measure	Value	
Filename	s_1.mm9_unaligned.txt	
File type	Conventional base calls	
Encoding	Sanger / Illumina 1.9	
Total Sequences	23594500	
Filtered Sequences	0	
Sequence length	25-51	
%GC	54	
>>END_MODULE

Options

output file
File name for output
table name column
Column that holds table names
column name column
Column that holds the column names
table data
Column that holds data

Input Ports

Icon
Table with string columns

Best Friends (Incoming)

Installation

To use this node in KNIME, install KNIME NGS tools 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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