pipe.PostAlignTasks | R Documentation |
Do secondary processing steps after running the alignment pipeline for a sample.
pipe.PostAlignTasks(sampleID, annotationFile = "Annotation.txt", optionsFile = "Options.txt",
dataType = c( "RNA-seq", "DNA-seq", "ChIP-seq", "RIP-seq"), verbose = TRUE)
sampleID |
the SampleID for this sample. This SampleID keys for a row of annotation details in the annotation file, for getting sample-specific details. The SampleID is also used as a sample-specific prefix for all files created during the processing of this sample. |
annotationFile |
the file of sample annotation details, which specifies all needed
sample-specific information about the samples under study.
See |
optionsFile |
the file of processing options, which specifies all processing
parameters that are not sample specific. See |
dataType |
the type of NGS data to be aligned, determines the folders/files that will be generated. |
Runs any optional secondary processing steps after the main alignment pipeline is
finished. Currently, the only optional step is the investigation of the the 'NoHit' reads
to see what unexpected organisms, etc., remain in the raw FASTQ files after alignment.
See option investigate.NoHits
and function pipe.CR_Investigate
.
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