10x fragment files come in a bed-like format, with columns chr, start, end, cell_id, and pcr_duplicates. Unlike a standard bed format, the format from cellranger has an inclusive end-coordinate, meaning the end coordinate itself is what should be counted as the tagmentation site, rather than offset by 1.
Usage
open_fragments_10x(path, comment = "#", end_inclusive = TRUE)
write_fragments_10x(
fragments,
path,
end_inclusive = TRUE,
append_5th_column = FALSE
)Arguments
- path
File path (e.g. fragments.tsv or fragments.tsv.gz)
- comment
Skip lines at beginning of file which start with comment string
- end_inclusive
Whether the end coordinate of the bed is inclusive – i.e. there was an insertion at the end coordinate rather than the base before the end coordinate. This is the 10x default, though it's not quite standard for the bed file format.
- fragments
Input fragments object
- append_5th_column
Whether to include 5th column of all 0 for compatibility with 10x fragment file outputs (defaults to 4 columns chr,start,end,cell)
