Up: Component summary
Up: Component summary
Component
STARGenomeSpliced 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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