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


STAR Options

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.
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.

Input Ports

Input depends on the runMode:
alignReads: FastQ file(s) loaded with FileLoader (single- and paired-reads are supported).
generateGenome: FastA file(s) loaded with FileLoader.

Output Ports

Cell 0: In case of alignReads path to SAM file, otherwise path to the folder containing the generated genome.


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