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)
Details
open_fragments_10x
No disk operations will take place until the fragments are used in a function
write_fragments_10x
Fragments will be written to disk immediately, then returned in a readable object.
Examples
## Download example fragments from pbmc 500 dataset and save in temp directory
data_dir <- file.path(tempdir(), "frags_10x")
dir.create(data_dir, recursive = TRUE, showWarnings = FALSE)
url_base <- "https://cf.10xgenomics.com/samples/cell-atac/2.0.0/atac_pbmc_500_nextgem/"
frags_file <- "atac_pbmc_500_nextgem_fragments.tsv.gz"
atac_raw_url <- paste0(url_base, frags_file)
if (!file.exists(file.path(data_dir, frags_file))) {
download.file(atac_raw_url, file.path(data_dir, frags_file), mode="wb")
}
#######################################################################
## open_fragments_10x() example
#######################################################################
frags <- open_fragments_10x(
file.path(data_dir, frags_file)
)
## A Fragments object imported from 10x will not have cell/chromosome
## information directly known unless written as a BPCells fragment object
frags
#> IterableFragments object of class "ShiftFragments"
#>
#> Cells: count unknown
#> Chromosomes: count unknown
#>
#> Queued Operations:
#> 1. Load 10x fragments file from /tmp/RtmpsGFdDm/frags_10x/atac_pbmc_500_nextgem_fragments.tsv.gz
#> 2. Shift start +0bp, end +1bp
frags %>% write_fragments_dir(
file.path(data_dir, "demo_frags_from_h5"),
overwrite = TRUE
)
#> IterableFragments object of class "FragmentsDir"
#>
#> Cells: 219780 cells with names CCACGTTCAGTAACTC-1, GCGAGAAGTCCACCAG-1 ... AAACGAAGTTCAGAAA-1
#> Chromosomes: 39 chromosomes with names chr1, chr10 ... KI270713.1
#>
#> Queued Operations:
#> 1. Read compressed fragments from directory /tmp/RtmpsGFdDm/frags_10x/demo_frags_from_h5
#######################################################################
## write_fragments_10x() example
#######################################################################
frags <- write_fragments_10x(
frags,
file.path(data_dir, paste0("new_", frags_file))
)
frags
#> IterableFragments object of class "ShiftFragments"
#>
#> Cells: count unknown
#> Chromosomes: count unknown
#>
#> Queued Operations:
#> 1. Load 10x fragments file from /tmp/RtmpsGFdDm/frags_10x/new_atac_pbmc_500_nextgem_fragments.tsv.gz
#> 2. Shift start +0bp, end +1bp
