dot-singleCounterUMI4C: Count UMIs for a given bam file.

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

Count UMIs for a given bam file.

Description

Count UMIs for a given bam file.

Usage

.singleCounterUMI4C(
  filtered_bam_R1,
  filtered_bam_R2,
  digested_genome_gr,
  pos_viewpoint,
  res_enz,
  count_dir,
  filter_bp = 1e+07
)

Arguments

filtered_bam_R1	R1 bam file.
filtered_bam_R2	R2 bam file.
digested_genome_gr	GRanges object containing the coordinates for the digested genome.
pos_viewpoint	Vector consist of chromosome, start and end position of the viewpoint.
res_enz	Character containing the restriction enzyme sequence.
count_dir	Counter directory.
filter_bp	Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6

Value

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

Pasquali-lab/UMI4Cats documentation built on March 23, 2024, 9:42 p.m.