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FeatureCounts

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

FeatureCounts is a highly efficient general-purpose read summarizing program that counts mapped reads to genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
FeatureCounts takes as input SAM/BAM files and an annotation file including chromosomal coordinates of features. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Source: http://bioinf.wehi.edu.au/featureCounts/

For more details, see: Liao et al, Bioinformatics 2013; doi: 10.1093/bioinformatics/btt656
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Options

Path to annotation file
Set the path to the GTF or SAF annotation file.
Path to output folder
Set the path to the folder where the output files will be generated.
Paired-end read options
Count fragments instead of reads: If specified, fragments (or templates) will be counted instead of reads.
Count chimeric fragments: If specified, chimeric fragments that have their two ends aligned to different chromosomes will be counted.
Further options
Feature type used for counting: Choose which feature type should be used for counting in the case a GTF file is used.
(Default: 'exon')
Count multimapped reads: Choose whether also not uniquely mapped reads should be counted.
Thread number: Set the number of threads to be used. [1-16]
Perform read summarization at the feature level: If specified, read summarization will be performed at the feature level (eg. exon level). Otherwise, it is performed at meta-feature level (eg. gene level)
Feature type used for grouping results: Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided.
(Default: 'gene_id'; This attribute type is usually the gene identifier.) This argument is useful for the meta-feature level summarization.

Preference page

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to featureCounts
Set the path to the compiled featureCounts binary. Theoretically all versions starting from 1.4.3 should be supported.

Input Ports

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Cell 0: One or more SAM or BAM files.

Output Ports

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Cell 0: Path to output file.

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

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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