Split fastq files at a given restriction site.

Source: R/contactsUMI4C.R

Split fastq files at a given restriction site.

.singleSplitUMI4C(
  fastq_file,
  res_enz,
  cut_pos,
  split_dir,
  min_flen = 20,
  numb_reads = 1e+09
)

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=1e9.

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.