pipe.SpliceAlign: Splice Alignment Pileline Step for NGS Data

Description Usage Arguments Details Value Author(s) See Also

Description

Runs the optional third splice alignment step to place reads from FASTQ files onto splice junctions.

Usage

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pipe.SpliceAlign(inputFastqFile, sampleID, annotationFile = "Annotation.txt",
	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.

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.

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 splice junction index specified in the options file. Reads that do align are written to a BAM file in the splicing results subfolder. Reads that fail to align are written to temporary file(s) in the current working folder.

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


robertdouglasmorrison/DuffyNGS documentation built on Dec. 14, 2018, 3:04 p.m.