shift 5' ends — shiftGAlignmentsList • ATACseqQC

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.

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

Arguments

gal	An object of GAlignmentsList.
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. The PCR duplicated will be removed unless there is metadata keepDuplicates set to TRUE.

Author

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, which=which, asMates=TRUE)
objs <- shiftGAlignmentsList(gal)
export(objs, "shift.bam")