counterUMI4C: UMI counting

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

UMI counting

Description

Algorithm for counting and collapsing the number of UMIs supporting a specific ligation.

Usage

counterUMI4C(
  wk_dir,
  pos_viewpoint,
  res_enz,
  digested_genome,
  filter_bp = 1e+07
)

Arguments

wk_dir	Working directory where to save the outputs generated by the UMI-4c analysis.
pos_viewpoint	GRanges object containing the genomic position of the viewpoint.
res_enz	Character containing the restriction enzyme sequence.
digested_genome	Path for the digested genome file generated using the digestGenome function.
filter_bp	Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6.

Details

For collapsing different molecules into the same UMI, takes into account the ligation position and the number of UMI sequence mismatches.

Value

Creates a compressed tab-delimited file in wk_dir/count named "basename(fastq) _counts.tsv.gz", containing the coordinates for the viewpoint fragment, contact fragment and the number of UMIs detected in the ligation.

Examples

if (interactive()) {
path <- downloadUMI4CexampleData(reduced = TRUE)

hg19_dpnii <- digestGenome(
    cut_pos = 0,
    res_enz = "GATC",
    name_RE = "DpnII",
    sel_chr = "chr16", # digest only chr16 to make example faster
    ref_gen = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
    out_path = file.path(path, "digested_genome")
)

viewpoint <- GenomicRanges::GRanges("chr16:10972515-10972548")

counterUMI4C(
    wk_dir = file.path(path, "CIITA"),
    pos_viewpoint = viewpoint,
    res_enz = "GATC",
    digested_genome = hg19_dpnii
)

}

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.