dot-singleSplitUMI4C: Split fastq files at a given restriction site.

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

Description

Split fastq files at a given restriction site.

Usage

.singleSplitUMI4C(
  fastq_file,
  res_enz,
  cut_pos,
  split_dir,
  min_flen = 20,
  numb_reads
)

Arguments

fastq_file	Fastq file path.
res_enz	Character containing the restriction enzyme sequence.
cut_pos	Numeric indicating the nucleotide position where restriction enzyme cuts (zero-based) (for example, for DpnII is 0).
split_dir	Directory where to save split files.
min_flen	Minimal fragment length to use for selecting the fragments. Default=20
numb_reads	Number of lines from the FastQ file to load in each loop. If having memory size problems, change it to a smaller number. Default=10e10.

Value

Creates a compressed FASTQ file in wk_dir/split named basename(fastq)).fq.gz, containing the split reads based on the restriction enzyme used.

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