R: Count fragment overlaps when sequencing was performed from...
countFragmentOverlapsSecondCutter
R Documentation
Count fragment overlaps when sequencing was performed from the second
cutting site
Description
countFragmentOverlapsSecondCutter counts the number of reads mapping to
each cutting site of the second cutter and then summarizes them over the
fragment ends of the first cutter stored in rowRanges of the
FourC object.
Defines whether the read start should be extended by the length
of the second cutter recognition sequence to overlap the cutting sites which is
required for counting. If the cutting site has been trimmed with the primer
sequence this has to be set to TRUE. Default is TRUE.
minMapq
Minimum mapping quality required for counting the read.
Default is 0. If set to negative values the filtering step is skipped.
shift
Maximum difference in starts or ends between read and fragment
positions. Default is 0.
Value
Updated FourC object that contains two new assayscountsLeftFragmentEnd and countsRightFragmentEnd with the
count values at the respective fragment end.