pipe.PreAlignTasks: Pre-Alignment Tasks

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

Pre-Alignment Tasks

Description

Do setup prior to running the alignment pipeline for a sample.

Usage

pipe.PreAlignTasks(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

Creates sub-folders for all results that will be generated by the pipeline, and pre-deletes any old previous results files for that SampleID prior to alignment.

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