For single end reads, an estimate of the frament
size. For paired reads, the fragment size can be directly computed
from the paired alignment and this value is ignored.
force.single.end
Treat all paired reads as single end. It is
generally a bad idea but may be useful in some rare situations. Only
use this option if you really know what you are doing.
Value
A GRanges object with count data.
Details
Largely derived from its equivalent function in the exomeCopy package.