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\name{makeAxtTracks}
\alias{makeAxtTracks}
\title{
makeAxtTracks
}
\description{
Make the bed tracks for the \sQuote{Axt} alignment.
}
\usage{
makeAxtTracks(x)
}
\arguments{
\item{x}{
A \code{Axt} object.
}
}
\details{
The coordinates of query \sQuote{Axt} alignment are fixed to be relative to
positive strand before output into \sQuote{bed} file.
}
\value{
A list of GRanges for target and query alignments.
The two output \sQuote{bed} files are
\dQuote{targetAxt.bed} and \dQuote{queryAxt.bed}.
}
\author{
Ge Tan
}
\seealso{
\code{\link{fixCoordinates}}
}
\examples{
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
axtFn <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn)
makeAxtTracks(axt)
}
|
