pipe.PostAlignTasks: Post-Alignment Tasks

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Post-Alignment Tasks

Description

Do secondary processing steps after running the alignment pipeline for a sample.

Usage

pipe.PostAlignTasks(sampleID, annotationFile = "Annotation.txt", optionsFile = "Options.txt", 
	dataType = c( "RNA-seq", "DNA-seq", "ChIP-seq", "RIP-seq"), verbose = TRUE)

Arguments

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 DuffyNGS_Annotation.
optionsFile	the file of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.
dataType	the type of NGS data to be aligned, determines the folders/files that will be generated.

Details

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.

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.