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STARGenome

Spliced Transcripts Alignment to a Reference for RNA-seq

See the STAR component for more documentation.

Meant for generating STAR genome. A genome is STAR terminology for a directory containing a transcriptome index.

Default values are set to generating a second pass genome from discovered splice junctions from a first pass of STAR 2-pass. In this case you do not need the annotation but just the spliceJunctions.

Consult STAR manual for options on generating the genome.

TODO: Add input for specifying all parameters in one file? There aren't that many parameters for generating genomes...

Version 0.1
Bundle sequencing
Categories Alignment
Authors Lauri Lyly (lauri.lyly@helsinki.fi)
Issue tracker View/Report issues
Requires STAR ; installer (bash)
Source files component.xml main.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
genomeFasta BinaryFile Mandatory If you are using this for a second pass, sequence should correspond to the main genome.
annotation BinaryFile Optional Genome annotation for splice junctions. A GTF file will work by default. For a GFF3 file add to genomeParameters: "--sjdbGTFtagExonParentTranscript Parent" Not needed for 2nd pass of STAR.
spliceJunctions CSV Optional Splice junctions produced from previous STAR alignment or manually. See the output field of STAR component for a description. Typically not needed for 1st pass of STAR.

Outputs

Name Type Description
genome BinaryFolder Genome with given splice junctions.

Parameters

Name Type Default Description
genomeParameters string "--sjdbOverhang 100" Parameters supplied when generating a genome. Default is enough for 2-pass STAR's second pass, without providing an annotation. Consult the parametersDefault file in STAR source, or STAR manual. Example: BIAS="--sjdbScore 3" (=2 by default) provides extra alignment score for alignments that cross database junctions. If this score is positive, it will bias the alignment toward annotated junctions.
threads int 1 Number of threads passed to STAR.

Test cases

Test case Parameters IN
genomeFasta
IN
annotation
IN
spliceJunctions
OUT
genome
case1 properties genomeFasta annotation (missing) (missing)

genomeParameters=--genomeSAindexNbases=5


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