getVDVnames: Identify VDV reads based on alignment of the vector on the...

In pgpmartin/NanoBAC: Analysis of long read (Oxford Nanopore, PacBio) data from BAC or large plasmid sequencing

Description

VDV reads contain vector-DNA-vector sequences. Only reads longer than minReadLength (>=2kb) can be annotated as VDV reads. VDV reads contain an alignment of the vector in their first 1kb and in their last 1kb but do not contain any alignment to the vector in the center region (i.e. excluding 1.15x the length of the vector on each side)

Usage

getVDVnames(alignGR, vectorLength, minReadLength = 2000, SideWidth = 1000)

Arguments

alignGR	a GRanges object containing the alignment of the vector on the reads
vectorLength	integer Length of the vector (in bp)
minReadLength	integer. Minimum read length to be a VDV read (defaults to 2kb)
SideWidth	integer. Length on each side of the read that must align to some extent to the vector

Value

a character vector of names of the VDV reads

Examples

## Create a GRanges. Only Read1 and Read2 are VDV reads
  rgr <- GenomicRanges::GRanges(c("Read1:1-2000", "Read1:98001-1e5",
                                  "Read2:100-1800", "Read2:99e3-1e5",
                                  "Read3:1e4-1.4e4"),
                                seqlengths = c("Read1"=1e5, "Read2"=1e5,
                                               "Read3"=2e4, "Read4"=5e4))
## Names of VDV reads:
  getVDVnames(rgr, 4000)

pgpmartin/NanoBAC documentation built on Dec. 11, 2020, 9:51 a.m.