Up: Component summary
Up: Component summary
Component
TrimmerTrim sequence reads at both ends.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Quality control |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | rnaSeq.jar (jar) |
| Source files | component.xml Trimmer.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| data | Array<BinaryFile> | Mandatory | Sequence files in FASTQ format. Use key "read" and "mate" if defining paired-end data, and just "read" if not. |
| perBaseSeqQual | Array<CSV> | Optional | Per base sequence quality. For pair-end data, the keys are "read" and "mate". For single-end data, the key is "read". Either "perBaseSeqQual" or "trimInfo" has to be set. |
| trimInfo | CSV | Optional | A CSV file records regions with good quality. The format follows the "trimInfo" output of 'SeqQC' component. Either "perBaseSeqQual" or "trimInfo" has to be set. |
Outputs| Name | Type | Description |
|---|---|---|
| trimmedReads | Array<BinaryFile> | An array for trimmed reads. The keys are "read" and "mate" for pair-end data and only "read" for single-end. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| paired | boolean | true | A boolean for pair-end data. The default is: true. |
| score | int | 30 | The quality threshold for trimming the reads. Regions with mean score per base lower than this threshold will be trimmed. The default is: 30. |
Test cases| Test case | Parameters▼ | IN data |
IN perBaseSeqQual |
IN trimInfo |
OUT trimmedReads |
|---|---|---|---|---|---|
| case1 | (missing) | data | (missing) | trimInfo | trimmedReads |
| case2 | (missing) | data | perBaseSeqQual | (missing) | trimmedReads |