Up: Component summary Function

SmallRNAQC

Performs 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)
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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.

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