Count UMIs for a given bam file.

Source: R/contactsUMI4C.R

Count UMIs for a given bam file.

.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.