shiftGAlignments: shift 5' ends for single end reads

In jianhong/ATACseqQC: ATAC-seq Quality Control

shift 5' ends for single end reads

Description

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.

Usage

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

Arguments

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.

Value

An object of GAlignments with 5' end shifted reads.

Author(s)

Jianhong Ou

Examples

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")

jianhong/ATACseqQC documentation built on Nov. 2, 2024, 12:08 a.m.