Up: Component summary Component

Trimmer

Trim 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

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