pipe.GenomicAlign: Genomic Alignment Pileline Step for NGS Data

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

Genomic Alignment Pileline Step for NGS Data

Description

Runs the genomic alignment step to place reads from FASTQ files onto genomic chromosomal locations.

Usage

pipe.GenomicAlign(inputFastqFile, sampleID, 
	optionsFile = "Options.txt", asMatePairs = FALSE, verbose = TRUE, 
	rawReadCount = NULL)

Arguments

inputFastqFile	character vector of one or more raw FASTQ files
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.
optionsFile	the file of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.
asMatePairs	logical flag, should the vector of FASTQ be treated as two mate pair files?
rawReadCount	optional argument of the number of reads in the files. By default this gets calculated on the fly.

Details

Aligns the given FASTQ files against the Bowtie2 genomic index specified in the options file. Reads that do align are written to a BAM file in the align results subfolder. Reads that fail to align are written to temporary file(s) in the current working folder for the optional subsequent splice alignment step.

Value

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

Also, a list of alignment counts:

RawReads	the number of reads in the raw FASTQ files
UniqueReads	the number of reads that aligned to exactly one location
MultiReads	the number of reads that aligned to two or more locations
NoHitReads	the number of reads that failed to align
Time	the time usage of this alignment step, as from proc.time

Author(s)

Bob Morrison

See Also

pipe.RiboClear Ribo clearing alignment against an index of unwanted genomic featurs. pipe.SpliceAlign Splice junction alignment against an index of standard and alternative splice junctions.

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