Up: Component summary
Up: Component summary
Function
SmallRNAQCPerforms all 3 quality filtering steps (preprocessing, alignment to genome, and optional alignment to transcripts) in the smallRNA pipelines.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Preprocessing smallRNA |
| Authors | Katherine Icay (katherine.icay@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | Java ; samtools ; jbzip2-0.9.jar (jar) ; sam-1.32.jar (jar) ; rnaSeq.jar (jar) |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| reads | FASTQ | Optional | Input file in FASTQ format. Required for QCstep1. |
| mates | FASTQ | Optional | Input file in FASTQ format. Required for QCstep1. |
| stats | CSV | Optional | List of per sample paths to stats output of smallRNAprep. Required for QCstep 1. |
| bam | BAM | Optional | Input file in BAM format. Required for QCstep 2 and 3. |
| mergeStats | CSV | Optional | Output stats of a previous QCstep to combine with current instance stats. Required for QCstep 2 and 3. |
Outputs| Name | Type | Description |
|---|---|---|
| qc | CSV | QC test results that can later be filtered by column pass = [T/F]. |
| report | Latex | A latex report produced by SeqQC on the sequence quality. Only produced with QCstep=1. |
| fastqc | BinaryFolder | Original output folder from FastQC. If QCstep=1 (currently redundant. See QCFasta instead). |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| QCstep | int | 2 | Filtering step to perform. 1 (redundant, see QCFasta instead) = FastQC on preprocessed reads (to use after smallRNAprep). 2 = samtools_flagstat on alignment to genome. 3 = samtools flagstat on alignment to Ensembl transcripts. |
| filePath | string | "" | Reference path of input stats file corresponding to reads sample. |
| suffix | string | "" | Reference key of input stats file corresponding to reads sample. |