shiftGAlignments: shift 5' ends for single end reads
In ATACseqQC: ATAC-seq Quality Control

Description Usage Arguments Value Author(s) Examples

shift the GAlignmentsLists by 5' ends. All reads aligning to the positive strand will be offset by +4bp, and all reads aligning to the negative strand will be offset -5bp by default.

1	shiftGAlignments(gal, positive = 4L, negative = 5L, outbam)

`gal`	An object of GAlignments.
`positive`	integer(1). the size to be shift for positive strand
`negative`	integer(1). the size to be shift for negative strand
`outbam`	file path to save shift reads. If missing, no file will be write.

An object of GAlignments with 5' end shifted reads.

Jianhong Ou

bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC")
tags <- c("AS", "XN", "XM", "XO", "XG", "NM", "MD", "YS", "YT")
library(BSgenome.Hsapiens.UCSC.hg19)
which <- as(seqinfo(Hsapiens)["chr1"], "GRanges")
gal <- readBamFile(bamfile, tag=tags, 
                   what=c("qname", "flag", "mapq", "seq", "qual"),
                   which=which, asMates=FALSE, bigFile=TRUE)
objs <- shiftGAlignments(gal)
export(objs, "shift.bam")