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• Downloading
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Documentation

• Quickstart Guide
• Design file v1
• Design file v2
• Workflow file
• Configuration file
• Built-in modules
  • Create mapper index
  • Create Minimap2 mapper index
  • Create STAR mapper index
  • FastQC
  • Filter reads
  • Map reads
  • Filter alignments
  • Filter and map
  • Sam2Bam
  • Bam2Sam
  • Sam2Fastq
  • Splice2Bed
  • Expression
  • Expression annotation
  • MultiQC
  • Normalization
  • Differential analysis
  • Differential analysis annotation
  • Differential analysis with DESeq2
  • Matrix to Cell Ranger Matrix
  • R SingleCellExperiment creator
  • Splitters and mergers
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• Cluster configuration
• Hadoop configuration
• Data repositories configuration
• Known bugs
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• Writing a Module plugin
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• Javadoc

Create STAR mapper index module

This module allow to create a STAR mapper index with custom options. If this module is not declared in the workflow file, the default mapper index generator will be used if you want to use STAR as mapper.

• Internal name: starindexgenerator
• Available: Both local and distributed mode


• Input ports:
  • genome: genome sequence file (format: genome_fasta)
  • genomedescription: genome description (automatically generated from genome sequence file)
  • annotation: genome annotation in GFF3 or GTF format (if required in parameters)


• Output port:
  • output: genome mapper index


• Mandatory parameters: none


• Optional parameters:

Parameter	Type	Description	Default value
overhang	integer	Specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database	100
use.gtf.file	boolean	If true, the GFF3 annotation specified in the design file will be used by STAR to extract splice junctions. Using this option greatly improve the accuracy of the mapping. It is highly recommanded to use this option when feature annotation is available.	None
file.chr.start.end	String	Path to the file that contains the list of splice junctions coordinates	None
gtf.feature.exon	String	Feature type (3rd column in GFF file) to be used	None
gtf.tag.exon.parent.transcript	String	GFF attribute to be used as feature ID	None
features.file.format	string	The features file format. Currently only GFF/GFF3 and GTF format are supported.	gff3
genome.sa.index.nbases	Integer	See STAR documentation for more information	None
genome.chr.bin.nbits	Integer	See STAR documentation for more information	None
use.expression.step.parameters	Boolean	Use the genomictype and attributeid parameters values from an expression step to set the values of the gtf.feature.exon and gtf.tag.exon.parent.transcript parameters of this step	False
indexer.arguments	String	Additional indexer arguments	Not set

• Configuration example:

<!-- Create STAR index -->
<step skip="false">
	<module>starindexgenerator</module>
	<parameters>
		<parameter>
			<name>overhang</name>
			<value>100</value>
		</parameter>
		<parameter>
			<name>use.gtf.file</name>
			<value>true</value>
		</parameter>
		<parameter>
			<name>use.expression.step.parameters</name>
			<value>true</value>
		</parameter>
	</parameters>
</step>