pipe.Alignment: Alignment Stage of DuffyNGS Pipeline workflow.

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

Alignment Stage of DuffyNGS Pipeline workflow.

Description

Turn FASTQ file(s) of raw reads into RiboCleared, Genomic, and SpliceJunction alignments. Encapsulates a 3 stage Bowtie alignment protocol for NGS data, to turn raw reads into alignments. First, an optional RiboClearing stage to remove ribosomal RNA and other high expression unwanted transcripts. Next the main genomic alignment stage to capture the reads of interest matching the target genome(s). Lastly, an optional splice alignment stage to capture reads spanning known splice junctions.

Usage

pipe.RNAalignment(sampleID = NULL, annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", verbose = TRUE)
pipe.DNAalignment(sampleID = NULL, annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", verbose = TRUE)
pipe.ChIPalignment(sampleID = NULL, annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", verbose = TRUE)
pipe.RIPalignment(sampleID = NULL, annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", verbose = TRUE)
pipe.Alignment(sampleID = NULL, annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", 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.

Details

Turn FASTQ file(s) of raw reads into 3 groups of alignments and a final group of 'NoHits' unaligned reads. Details affecting choice of alignment indexes and Bowtie2 runtime parameters are set in the DuffyNGS_Options file. Main pipeline components:

pipe.RiboClear Ribo clearing against an index of unwanted transcripts.

pipe.GenomicAlign Genomic alignment against an index of target genome(s).

pipe.SpliceAlign Splice junction alignment against an index of standard and alternative splice junctions.

This function is called as the alignment stage of the top level pipeline tool.

Value

a family of BAM files, FASTQ files, and summary files, written to subfolders under the top level results.path folder.

Also, a list of alignment counts:

nReadsIn	the number of reads in the raw FASTQ file
nNoHit	the number of reads that failed to align to any stage of the alignment pipeline
nRibo	the number of reads that aligned to the RiboClearing stage
nGenomic	the number of reads that aligned to the Genomic stage of the alignment pipeline
nSplice	the number of reads that aligned to the SpliceJunction stage of the alignment pipeline

Author(s)

Bob Morrison

robertdouglasmorrison/DuffyNGS documentation built on Sept. 1, 2024, 9:25 p.m.