dot-singlePrepUMI4C: Prepar fastq files at a given barcode.

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

Description

Prepar fastq files at a given barcode.

Usage

.singlePrepUMI4C(
  fq_R1,
  fq_R2,
  bait_seq,
  bait_pad,
  res_enz,
  prep_dir,
  numb_reads = 1e+11
)

Arguments

fq_R1	Fastq file R1.
fq_R2	Fastq file R2.
bait_seq	Character containing the bait primer sequence.
bait_pad	Character containing the pad sequence (sequence between the bait primer and the restriction enzyme sequence).
res_enz	Character containing the restriction enzyme sequence.
prep_dir	Prep directory.
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/prep named basename(Fastq)).fq.gz, containing the filtered reads with the UMI sequence in the header. A data.frame object with the statisitics is also returned.

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