Shift start or end coordinates — shift

Shifts start or end of fragments by a fixed amount, which can be useful to correct the Tn5 offset.

Usage

shift_fragments(fragments, shift_start = 0L, shift_end = 0L)

Arguments

fragments: Input fragments object
shift_start: How many basepairs to shift the start coords
shift_end: How many basepairs to shift the end coords

Value

Shifted fragments object

Details

The correct Tn5 offset is +/- 4bp since the Tn5 cut sites on opposite strands are offset by 9bp. However, +4/-5 bp is often applied to bed-format files, since the end coordinate in bed files is 1 past the last basepair of the sequenced DNA fragment. This results in a bed-like format except with inclusive end coordinates.