pipe.AlignToWig: Turn BAM Alignments into Wiggle Tracks.

Description Usage Arguments Details Value Author(s) See Also

Description

Pipeline step that generates the wiggle tracks of read pileups for one sample. The alignment BAM files are converted to R data objects that contain strand specific and unique/multi-hit wiggle track details to nucleotide resolution for all species and chromosomes in the current target.

Usage

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pipe.AlignToWig( sampleID, annotationFile = "Annotation.txt", optionsFile = "Options.txt", 
	results.path = NULL, dataType = "RNA-seq", 
	mode = c( "normal", "QuickQC", "spliceOnly"))

Arguments

sampleID

The SampleID for this sample.

annotationFile

File of sample annotation details, which specifies all needed sample-specific information about the samples under study. See DuffyNGS_Annotation.

optionsFile

File of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.

results.path

The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'.

dataType

The type of read data contained in the aligned BAM file.

mode

Controls the behavior of how alignments are loaded into the the wiggle track data objects. Optional mode "QuickQC" invokes the behavior for preliminary QC analysis. See pipe.QuickQC.

Details

This pipeline step turns the BAM files of alignment results into wiggle track data objects. It combines the genomic alignments BAM file with the optional splice junction alignments BAM file, to create the nucleotide resolution read depth information needed for later transcriptomes and read pileup image creation.

Value

A family of files is created on disk:

Wiggles

A file and subfolder of wiggle track data objects for this sample is written to the 'wig' subfolder of results. These contain the strand and unique/multihit details of all chromosomes for all species in the sample.

Author(s)

Bob Morrison

See Also

alignToWig for the low level function that does the real work.


robertdouglasmorrison/DuffyNGS documentation built on Dec. 7, 2018, 8:01 a.m.