Up: Component summary
Up: Component summary
Component
QCParserParse SeqQC summary result.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Quality control |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml QCParser.pl |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| summary | Array<BinaryFile> | Mandatory | FASTQ file containing unpaired reads or the #1 mates for paired-end input. |
Outputs| Name | Type | Description |
|---|---|---|
| basicStats | Array<CSV> | Basic stats. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| perBaseSeqQual | Array<CSV> | Per base sequence quality. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| perSeqQualScore | Array<CSV> | Per sequence quality scores. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| perBaseSeqContent | Array<CSV> | Per base sequence content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| perBaseGC | Array<CSV> | Per base GC content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| perSeqGC | Array<CSV> | Per sequence GC content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| perBaseN | Array<CSV> | Per base N content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| seqDuplicateLevel | Array<CSV> | Sequence duplicate levels. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
| overrepresented | Array<CSV> | Overrepresented sequences. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| paired | boolean | true | A boolean for pair-end data. The default is: true. |
Test cases| Test case | Parameters▼ | IN summary |
OUT basicStats |
OUT perBaseSeqQual |
OUT perSeqQualScore |
OUT perBaseSeqContent |
OUT perBaseGC |
OUT perSeqGC |
OUT perBaseN |
OUT seqDuplicateLevel |
OUT overrepresented |
|---|---|---|---|---|---|---|---|---|---|---|---|
| case1 | (missing) | summary | basicStats | perBaseSeqQual | perSeqQualScore | perBaseSeqContent | perBaseGC | perSeqGC | perBaseN | seqDuplicateLevel | overrepresented |
| case2 | properties | summary | basicStats | perBaseSeqQual | perSeqQualScore | perBaseSeqContent | perBaseGC | perSeqGC | perBaseN | seqDuplicateLevel | overrepresented |
|
paired=false |
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| case3 | properties | summary | basicStats | perBaseSeqQual | perSeqQualScore | perBaseSeqContent | perBaseGC | perSeqGC | perBaseN | seqDuplicateLevel | overrepresented |
|
paired=false |
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