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.

Examples

## Prep data
frags <- tibble::tibble(
  chr = "chr1",
  start = seq(10, 260, 50),
  end = start + 30,
  cell_id = paste0("cell1")
) %>% as("GRanges")
frags
#> GRanges object with 6 ranges and 1 metadata column:
#>       seqnames    ranges strand |     cell_id
#>          <Rle> <IRanges>  <Rle> | <character>
#>   [1]     chr1     10-40      * |       cell1
#>   [2]     chr1     60-90      * |       cell1
#>   [3]     chr1   110-140      * |       cell1
#>   [4]     chr1   160-190      * |       cell1
#>   [5]     chr1   210-240      * |       cell1
#>   [6]     chr1   260-290      * |       cell1
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

frags <- frags %>% convert_to_fragments()


## Shift fragments
shift_fragments(frags, shift_start = 4, shift_end = -4) %>% as("GRanges")
#> GRanges object with 6 ranges and 1 metadata column:
#>       seqnames    ranges strand |  cell_id
#>          <Rle> <IRanges>  <Rle> | <factor>
#>   [1]     chr1     14-36      * |    cell1
#>   [2]     chr1     64-86      * |    cell1
#>   [3]     chr1   114-136      * |    cell1
#>   [4]     chr1   164-186      * |    cell1
#>   [5]     chr1   214-236      * |    cell1
#>   [6]     chr1   264-286      * |    cell1
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths