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

Description Usage Arguments Value

Description

Count UMIs for a given bam file.

Usage

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.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.


UMI4Cats documentation built on Dec. 31, 2020, 2:01 a.m.