Star

STAR, a "splice aware" RNA-seq aligner, aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Details are described in the publication: STAR: ultrafast universal RNA-seq aligner
Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635

Options

STAR Options

runMode

alignReads or generateGenome:

alignReads: Aligns reads to a reference genome.
generateGenome: Generates a genome index using one or more fastA files.

Use 2pass mapping?

For the most sensitive novel junction discovery, it is recommended to run STAR in the 2-pass mode. It does not increase the number of detected novel junctions, but allows to detect more spliced reads mapping to novel junctions.

Number of threads

Number of threads to run STAR genomeGenerate or alignReads.

Optional parameters

Parameters can be set like you would normally use them on the command line for this binary.

Path to genome indexes

Path to the genome directory where genome indeces were generated using the STAR generateGenome mode. This option is only needed when applying the alignReads mode.

Path to GTF file

Path to the file with annotated transcripts in the standard GTF format. STAR will extract splice junctions from this file and use them to greatly improve accuracy of the mapping. While this is optional, and STAR can be run without annotations, using annotations is highly recommended whenever they are available.

Overhang

The overhang specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. Ideally, this length should be equal to the ReadLength-1, where ReadLength is the length of the reads. For instance, for Illumina 2x100b paired-end reads, the ideal value is 100-1=99. In case of reads of varying length, the ideal value is max(ReadLength)-1. In most cases, the default value of 100 will work as well as the ideal value.

Path to output folder

Path where all the output data is stored. The folder of the input files is used if no path is specified or the given path is invalid.

Views

STDOUT / STDERR

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

Workflows

• KNIME4NGS_Test_DiffExpressionKnime4NGS

Links

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Developers