RawReadManipulator

This node is based on the RawReadManipulator tool (written by Jonathan Hoser). It filter reads from a fastQ or fastA file and creates a new fastQ/fastA file in the same directory, unless otherwise specified.

Options

Filter settings file

Choose whether to use filter settings calculated by FASTQC (in-port) or to specify your own filter settings file. If you decide to use your own filter settings, you have to set the path to the filter settings file.

Barcode file

Choose whether to split and trim reads by barcode. The barcodes must be specified in a BARCODE file
Barcodes should have the following format:
ID BARCODE(line End)
'#' marks a commentline

Parameters

Remove Adapters

This option enables you to remove adapters from reads (start and end only). Specify adapters in a comma-separated list (e.g "CAGGTACG,CATTTTAG,AAATTGGAC").

Trim 3'/5' Poly-A/T prefixes

This option can be covered by the filter settings.
Specify whether PolyA/T prefixes/tails at the 5' end or PolyA/T at the 3' end of the reads should be trimmed.

Discard reads with average quality below threshold

This option enables you to define a minimum average threshold in order to remove reads with low quality. Reads with an average read quality (mean over all single read-bases) below the defined threshold are discarded

Trim reads from right until quality threshold is reached

This option enables to trim reads by quality by defining a quality threshold. The reads can either be trimmed from only the right or from both sided ('Also trim from left') until a quality value above the set threshold is encountered. Also trim from left"> Reads are trimmed from both sides applying the threshold set in "Trim reads by quality"

Reads containing Ns

Determine whether to remove reads containing unknown bases (Ns).

Keep single ends if partner is discarded

In case of paired-end data sets you can define whether to keep single ends even though the partner is discarded.

Discard reads shorter than a given length

This option enables you to discard reads of a length shorter than a define minimum read length. This trimming process is performed after all other trimming operations.

Options for Illumina-data

In case of Illumina data: Specify the quality encoding, if known. If its set to 'auto', the node will make an educated guess.
Define whether the quality encoding should be converted to phred-based qualities.

Thread number

Set the number of threads be used.

Optional output folder for RRM

Choose whether the output files should be stored in a separate output folder. In this case set the path to the folder.

Preference page

HTE

Set a threshold for repeated execution.Only used if HTE is enabled in the preference page.

Views

STDOUT / STDERR

The node offers a direct view of its standard out and the standard error of the tool.

Workflows

• KNIME4NGS_Test_VarCallingKnime4NGS

Links

• No links available

Developers