splitDVDreads: Select DVD reads from a set of Nanopore reads and split the...

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

Description

The function does the following:

• Selects DVD readsThis is done using FilterBACreads

• Split the read sequence in DV and VDBased on vector alignment, split the read sequence in DV and VD

• Filter based on sizeKeep only the split reads with a DNA fragment that is at least MinDNAlengthbp long

• reverse complement reads on minus strandstrand is determined based on vector alignment

• Return the split readsThe split reads are returned as a DNAString object

By default, if alignemnt to the host genome is provided in the ReadClass object (column HostAlign), then the selected DVD reads are selected to not show any significant alignment to the host genome

Usage

splitDVDreads(
  ReadClass = NULL,
  blastvec = NULL,
  FastaFile = NULL,
  WithGeneA = NULL,
  WithGeneB = NULL,
  MinDNAlength = 10000L
)

Arguments

ReadClass	Either a tibble obtained with the AnnotateBACreads function or a path to an rds file containing such a file
blastvec	Either a table imported with readBlast or a path to a blast file obtained by aligning th evectors on the reads and using -outfmt 6
FastaFile	Either a DNAStringSet object containing the full read sequences or a path to a fasta file containing these sequences
WithGeneA	Logical. Should the VDV reads align with GeneA? Default is NULL, i.e. no filtering on GeneA alignment
WithGeneB	Logical. Should the VDV reads align with GeneB? Default is NULL, i.e. no filtering on GeneB alignment
MinDNAlength	Integer. Minimum length of the DNA fragment to keep the reads in the results

Value

A list with:

• ReadDefinition a DNAStringSet with the split reads

• ReadSequence a GRanges object with the definition of the DV/VD reads

Note that reads with alignment on the opposite strand of the vector ("-" strand) are automatically reverse complemented If no reads are selected, the function returns NULL and a warning.

Author(s)

Pascal GP Martin

Examples

## For simplicity (and to limit file size) we only keep the data for 5 pre-selected DVD reads
## Path to file (.rds) created with the AnnotateBACreads function
pathRC <- system.file("extdata", "BAC02_ReadClass.rds", package = "NanoBAC")
RC <- readRDS(pathRC)
selectedReads <- c("BAC02R5572", "BAC02R21438", "BAC02R1152",
                   "BAC02R20794", "BAC02R6278" )
RC <- RC[RC$ReadName %in% selectedReads,]
## Path to a fasta file containing the sequence of the 5 DVD reads
pathFasta <- system.file("extdata", "BAC02_5DVDreads.fa", package = "NanoBAC")
## Path to the file containing the result from the Blast alignment of the vector on the reads
pathBlast <- system.file("extdata", "BAC02_BlastVector.res", package = "NanoBAC")
## Select DVD reads and split the reads
myDVDreads <- splitDVDreads(ReadClass = RC,
                            blastvec = pathBlast,
                            FastaFile = pathFasta,
                            WithGeneA = TRUE,
                            WithGeneB = TRUE,
                            MinDNAlength = 35000)
## Read sequences:
myDVDreads$ReadSequence
## Read definitions:
myDVDreads$ReadDefinition

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